4V9F

The re-refined crystal structure of the Haloarcula marismortui large ribosomal subunit at 2.4 Angstrom resolution: more complete structure of the L7/L12 and L1 stalk, L5 and LX proteins

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Revisiting the Haloarcula marismortui 50S ribosomal subunit model.

Gabdulkhakov, A., Nikonov, S., Garber, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 997-1004

  • DOI: https://doi.org/10.1107/S0907444913004745
  • Primary Citation of Related Structures:  
    4V9F

  • PubMed Abstract: 

    The structure of the large ribosomal subunit from the halophilic archaeon Haloarcula marismortui (Hma) is the only crystal structure of an archaeal ribosomal particle that has been determined to date. However, the first model of the Hma 50S ribosomal subunit contained some gaps: the structures of functionally important mobile lateral protuberances were not visualized. Subsequently, some parts of the P (L12) stalk base were visualized at 3.0 Å resolution [Kavran & Steitz (2007), J. Mol. Biol. 371, 1047-1059]: the RNA-binding domain of r-protein P0 (L10), the C-terminal domain of L11 and helices 43 and 44 of the 23 S rRNA. Here, the 2.4 Å resolution electron-density map of the Hma 50S ribosomal subunit was revisited and approximately two-thirds of the P0 protein, residues 1-58 of the N-terminal domains of two P1 protein molecules, residues 130-156 of L11, the full-length r-protein LX, nucleotides 2137-2149 and 2226-2237 of the 23S rRNA helix H76 forming the L1 stalk, nucleotides 2339-2343 of the 23S rRNA (contacting L5 protein) and loops 29-34 and 108-128 of protein L5 could be visualized. Thus, this paper provides a supplemented version of the Hma 50S ribosomal subunit model.

    • Organizational Affiliation: 

    Institute of Protein Research, RAS, Pushchino, Moscow Region 142290, Russian Federation. azat@vega.protres.ru


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]240Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]338Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PE [auth C]246Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]120Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EI [auth G]255Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]177Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11PK [auth I]162Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PL [auth J]145Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PM [auth K]132Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PN [auth L]165Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eO [auth M]196Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PP [auth N]187Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eQ [auth O]116Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eR [auth P]149Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eS [auth Q]96Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PT [auth R]155Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PU [auth S]85Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PV [auth T]120Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24eW [auth U]67Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PX [auth V]71Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PY [auth W]154Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth X]92Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32eAA [auth Y]241Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeBA [auth Z]92Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eCA [auth 1]57Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eDA [auth 2]50Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44eEA [auth 3]92Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L12FA [auth 4],
GA [auth 5]		70Haloarcula marismortui ATCC 43049Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein LXHA [auth 6]56Haloarcula marismortui ATCC 43049Mutation(s): 0 
UniProt
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD
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BK [auth U],
IK [auth Z],
JK [auth 1],
LK [auth 3],
QJ [auth O]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACY
Query on ACY
Download Ideal Coordinates CCD File 
CK [auth W],
LI [auth 0],
MI [auth 0],
NI [auth 0]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
KI [auth 0],
ME [auth 0],
TJ [auth O]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
AJ [auth G]
EJ [auth J]
EK [auth Y]
FJ [auth J]
GH [auth 0]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
AI [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
AF [auth 0]
AG [auth 0]
AH [auth 0]
BF [auth 0]
BG [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.66α = 90
b = 299.67β = 90
c = 573.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-06-28
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description