9F1D

Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history. 


Literature

NAC guides a ribosomal multienzyme complex for nascent protein processing.

Lentzsch, A.M., Yudin, D., Gamerdinger, M., Chandrasekar, S., Rabl, L., Scaiola, A., Deuerling, E., Ban, N., Shan, S.O.

(2024) Nature 633: 718-724

  • DOI: https://doi.org/10.1038/s41586-024-07846-7
  • Primary Citation of Related Structures:  
    9F1B, 9F1C, 9F1D

  • PubMed Abstract: 

    Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively 1 . Both modifications are strictly cotranslational and essential in higher eukaryotic organisms 1 . The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex 2,3 (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K 4,5 (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.

    • Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21B [auth BT]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29C [auth Bb]245Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12D [auth Bt]165Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17F [auth Aq]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13I [auth Ar]151Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22K [auth BU]128Oryctolagus cuniculusMutation(s): 5 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19L [auth As]145Oryctolagus cuniculusMutation(s): 2 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2M [auth BA]257Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23N [auth BV]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10O [auth At]119Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3P [auth BB]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22Q [auth BP]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26R [auth BY]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aS [auth Av]130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18T [auth B]297Oryctolagus cuniculusMutation(s): 2 
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Find proteins for G1SZF4 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23U [auth BX]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18V [auth BQ]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27W [auth BZ]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23X [auth Aw]143Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6Y [auth BE]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth BW]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21AA [auth Au]83Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aBA [auth Ba]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CA [auth Ax]130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL30DA [auth BF]247Oryctolagus cuniculusMutation(s): 4 
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Find proteins for G1TUB1 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19EA [auth BR]196Oryctolagus cuniculusMutation(s): 3 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2FA [auth AZ]294Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25GA [auth Ay]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8HA [auth BG]266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4IA [auth BC]412Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20JA [auth BS]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aKA [auth Aa]264Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41LA [auth Az]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9MA [auth BH]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1NA [auth EA]386Homo sapiensMutation(s): 1 
Gene Names: METAP1, KIAA0094
EC: 3.4.11.18
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GTEx:  ENSG00000164024 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5OA [auth Ab]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30PA [auth Bc]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10QA [auth BI]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaRA [auth Ct]238Homo sapiensMutation(s): 0 
Gene Names: NACA, HSD48
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GTEx:  ENSG00000196531 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3SA [auth Ac]281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31TA [auth Bd]125Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11UA [auth BJ]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3VA [auth Cu]162Homo sapiensMutation(s): 0 
Gene Names: BTF3, NACB, OK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4WA [auth Ad]263Oryctolagus cuniculusMutation(s): 4 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32XA [auth Be]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainYA [auth BK]27Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetyltransferase 50,N-alpha-acetyltransferase 50ZA [auth DA]403Schistosoma japonicum, Homo sapiens
This entity is chimeric		Mutation(s): 0 
EC: 2.5.1.18 (PDB Primary Data), 2.3.1.258 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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PHAROS:  Q9GZZ1
GTEx:  ENSG00000121579 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5AB [auth Ae]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aBB [auth Bf]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13CB [auth BL]211Oryctolagus cuniculusMutation(s): 2 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunit915Homo sapiensMutation(s): 0 
Gene Names: NAA15, GA19, NARG1, NATH, TBDN100
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GTEx:  ENSG00000164134 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EB [auth Af]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34FB [auth Bg]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14GB [auth BM]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 10HB [auth DC]235Homo sapiensMutation(s): 2 
Gene Names: NAA10, ARD1, ARD1A, TE2
EC: 2.3.1.255
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GTEx:  ENSG00000102030 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7IB [auth Ag]432Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JB [auth Bh]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15KB [auth BN]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Huntingtin-interacting protein KLB [auth DD]228Homo sapiensMutation(s): 0 
Gene Names: HYPK, C15orf63, HSPC136
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GTEx:  ENSG00000242028 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8MB [auth Ah]208Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36NB [auth Bi]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13OB [auth BO]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9QB [auth Ai]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RB [auth Bj]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27SB [auth AA]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinTB [auth Aj]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth Bk]70Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28VB [auth AB]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11WB [auth Ak]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeXB [auth Bl]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aYB [auth AC]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12ZB [auth Al]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinAC [auth Bm]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30BC [auth AD]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13CC [auth Am]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42DC [auth Bo]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26EC [auth AE]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11FC [auth An]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aGC [auth Bp]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1HC [auth AF]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19IC [auth Ao]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28JC [auth Br]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29KC [auth AG]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9LC [auth Ap]172Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10MC [auth Bs]318Oryctolagus cuniculusMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
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KY [auth DB]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP
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RW [auth B7]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SPM
Query on SPM
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PI [auth B5],
UN [auth B5],
WAA [auth A2]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
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BE [auth B5]
BH [auth B5]
BZ [auth A2]
CO [auth B5]
EK [auth B5]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN
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EFA [auth Bj]
HFA [auth AC]
IFA [auth Bm]
JFA [auth Bo]
LFA [auth AE]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
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AAA [auth A2]
ACA [auth A2]
ADA [auth A2]
AEA [auth A2]
AF [auth B5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
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ABA [auth A2]
AD [auth B5]
AE [auth B5]
AH [auth B5]
AK [auth B5]
UNKNOWN ATOM OR ION
X
Modified Residues  8 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ		C [auth Bb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
SAC
Query on SAC		I [auth Ar]L-PEPTIDE LINKINGC5 H9 N O4SER
NMM
Query on NMM		L [auth As]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
V5N
Query on V5N		M [auth BA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC		P [auth BB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
HY3
Query on HY3		X [auth Aw]L-PEPTIDE LINKINGC5 H9 N O3PRO
AYA
Query on AYA		IA [auth BC]L-PEPTIDE LINKINGC5 H9 N O3ALA
M3L
Query on M3L		AC [auth Bm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Currently 9F1D does not have a validation slider image.



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesR35 GM136321
German Research Foundation (DFG)GermanySFB969/A01 and A07
Swiss National Science FoundationSwitzerland310030_212308
Swiss National Science FoundationSwitzerland51NF40-205601
European Research Council (ERC)European UnionSynergy Grant 101072047

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 2.0: 2024-09-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-02
    Changes: Data collection, Database references