9E16 | pdb_00009e16

Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 70S ribosome carrying an E-tRNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis

Majumdar, S., Li, Y., Manjari, S.R., Gamper, H.B., Hou, Y.M., Banavali, N.K., Ojha, A.K., Agrawal, R.K.

(2024) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 2,285.89 kDa 
  • Atom Count: 146,413 
  • Modeled Residue Count: 10,290 
  • Deposited Residue Count: 11,233 
  • Unique protein chains: 50
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein bL37B [auth 7]24Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome-tunnel occlusion factor (RTOF)C [auth 1]62Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32D [auth 0]57Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34E [auth 2]47Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35F [auth 3]64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36G [auth 4]37Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31H [auth 6]80Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2K [auth C]280Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3L [auth D]217Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4M [auth E]223Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5N [auth F]187Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6O [auth G]179Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L9P [auth H]152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13Q [auth J]195Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14R [auth K]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15S [auth L]146Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16T [auth M]138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17U [auth N]180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18V [auth O]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19W [auth P]113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20X [auth Q]129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21Y [auth R]104Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A2I7W9M4 (Mycobacterium tuberculosis)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Z [auth S]197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AA [auth T]100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BA [auth U]105Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25CA [auth V]215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27DA [auth W]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29EA [auth Y]77Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FA [auth Z]65Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28 C-GA [auth y]78Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth d]201Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth e]220Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth f]96Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]132Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11MA [auth k]139Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12NA [auth l]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15OA [auth o]89Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16PA [auth p]162Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17QA [auth q]135Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20RA [auth t]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S22SA [auth x]33Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18 C-TA [auth r]88Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3UA [auth c]274Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7VA [auth g]156Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9WA [auth i]151Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10XA [auth j]101Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13YA [auth m]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth s]93Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 C-AB [auth 9]101Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 C-BB [auth b]54Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
E-tRNAA [auth n]77Mycobacterium tuberculosis
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S ribosomal RNA3,138Mycobacterium tuberculosis
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Entity ID: 10
MoleculeChains LengthOrganismImage
5S ribosomal RNAJ [auth B]115Mycobacterium tuberculosis
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S ribosomal RNAHA [auth a]1,537Mycobacterium tuberculosis
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Entity ID: 55
MoleculeChains LengthOrganismImage
mRNACB [auth X]26Mycobacterium tuberculosis
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.4.0
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI32422

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-02
    Type: Initial release