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 5A9Z | pdb_00005a9z

Complex of Thermous thermophilus ribosome bound to BipA-GDPCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.2 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: 2,236.39 kDa 
  • Atom Count: 150,547 
  • Modeled Residue Count: 11,326 
  • Deposited Residue Count: 11,326 
  • Unique protein chains: 52
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L1C [auth AC]228Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth AD]272Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth AE]206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth AF]208Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth AG]182Thermus thermophilus HB8Mutation(s): 0 
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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 L10I [auth AI]153Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11J [auth AJ]134Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth AK]139Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth AL]122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth AM]145Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q72I23 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth AN]136Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17O [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: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth AP]110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth AQ]117Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth AR]117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth AS]101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth AT]110Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth AU]94Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth AV]110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth AW]180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth AX]85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth AY]67Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q9LCY4 (Thermus thermophilus)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth AZ]59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AA [auth Aa]71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth Ab]57Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth Ac]49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth Ad]49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth Ae]64Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth Af]37Thermus thermophilus HB8Mutation(s): 0 
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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 
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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 
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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 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth BP]124Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth BQ]114Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth BR]60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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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 
UniProt
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UniProt GroupP62238
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth BU]104Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P62658 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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UniProt GroupP62658
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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 P80382 (Thermus thermophilus)
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UniProt GroupP80382
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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 P62660 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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UniProt GroupP62660
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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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UniProt GroupP80380
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxBB [auth BY]24Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
BipACB [auth CA]593Thermus 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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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 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: 2016-02-03
    Changes: Database references, Other
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 2.0: 2018-10-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-18
    Changes: Other
  • Version 2.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary