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 5AA0 | pdb_00005aa0

Complex of Thermous thermophilus ribosome (A-and P-site tRNA) bound to BipA-GDPCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.8 of the entry. See complete history. 

Literature

Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.

Kumar, V., Chen, Y., Ero, R., Ahmed, T., Tan, J., Li, Z., Wong, A.S.W., Bhushan, S., Gao, Y.

(2015) Proc Natl Acad Sci U S A 112: 10944-10949

  • DOI: https://doi.org/10.1073/pnas.1513216112
  • Primary Citation Related Structures: 
    5A9V, 5A9W, 5A9X, 5A9Y, 5A9Z, 5AA0

  • PubMed Abstract: 

    BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.


  • Organizational Affiliation: 
    • Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore.

Macromolecule Content 

  • Total Structure Weight: 2,311.02 kDa 
  • Atom Count: 155,482 
  • Modeled Residue Count: 11,564 
  • Deposited Residue Count: 11,564 
  • Unique protein chains: 52
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth AC]228Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72GV9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AD]272Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I07 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AE]206Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I04 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AF]208Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AG]182Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth AH]174Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth AK]139Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth AL]122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth AM]145Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth AN]136Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth AO]117Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I33 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth AP]110Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I20 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth AQ]117Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72JU9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth AR]117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth AS]101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72HR2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth AT]110Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth AU]94Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I06 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth AV]110Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I15 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth AW]180Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72IA7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth AX]85Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth AY]67Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9LCY4 (Thermus thermophilus)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth AZ]59Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72I22 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31Y [auth Aa]71Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q72JR0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth Ab]57Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth Ac]49Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth Ad]49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth Ae]64Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth Af]37Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EA [auth AI]153Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11FA [auth AJ]134Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown peptideGA [auth Ag]128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth BF]234Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth BG]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth BH]208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth BI]150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth BJ]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth BK]155Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth BL]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth BM]127Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth BN]98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth BO]119Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth BP]124Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth BQ]114Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth BR]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth BS]88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth BT]83Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth BU]104Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth BV]73Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SLQ0
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth BW]80Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth BX]99Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxBB [auth BY]24Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding proteinFB [auth BZ]605Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth AA]2,889Thermus thermophilus HB8
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth AB]123Thermus thermophilus HB8
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S ribosomal RNAHA [auth BA]1,515Thermus thermophilus HB8
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Entity ID: 55
MoleculeChains LengthOrganismImage
tRNA chain 1CB [auth BC]76Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNA chain 2DB [auth BD],
EB [auth BE]
75Thermus thermophilus HB8
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Reference Sequence

Small Molecules

Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Other
  • Version 1.2: 2016-02-03
    Changes: Database references, Other
  • Version 1.3: 2017-08-30
    Changes: Advisory, Data collection, Structure summary
  • Version 1.4: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2018-10-03
    Changes: Data collection, Derived calculations
  • Version 1.6: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.7: 2019-12-18
    Changes: Other
  • Version 1.8: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary