9SK8 | pdb_00009sk8

Model of M. pneumoniae 30S IF1/2/3 tRNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation

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

Literature

Visual proteomics of translational control in a minimal bacterium

Dobbs, J.M., Jensen, R.K., Mahamid, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 876.94 kDa 
  • Atom Count: 58,879 
  • Modeled Residue Count: 4,826 
  • Deposited Residue Count: 4,845 
  • Unique protein chains: 23
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2C [auth A]249Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75560 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3D [auth B]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41205 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4E [auth C]203Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P46775 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5F [auth D]153Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50301 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6G [auth E]167Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75543 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7H [auth F]154Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75545 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8I [auth G]141Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50304 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9J [auth H]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75179 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10K [auth I]101Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75581 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11L [auth J]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50296 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12M [auth K]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75546 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13N [auth L]118Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50297 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14O [auth M]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50305 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15P [auth N]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75173 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16Q [auth O]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for A0A0H3DLS7 (Mycoplasmoides pneumoniae (strain ATCC 15531 / DSM 23978 / CIP 103766 / NBRC 14401 / NCTC 10119 / FH))
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17R [auth P]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50309 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18S [auth Q]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75541 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19T [auth R]84Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75576 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20U [auth S]77Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75237 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21V [auth T]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P57079 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3W [auth U]163Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78024 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor IF-1X [auth V]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50298 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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UniProt GroupQ50298
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2Y [auth W]584Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75590 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75590 
Go to UniProtKB:  P75590
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UniProt GroupP75590
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth 5]1,492Mycoplasmoides pneumoniae M129
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Entity ID: 2
MoleculeChains LengthOrganismImage
Initiator fMet-tRNAfMetB [auth 6]70Mycoplasmoides pneumoniae M129
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONM

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chan Zuckerberg InitiativeUnited States2021-234620
Independent Research Fund Denmark - Medical SciencesDenmark0106-00010A

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-23
    Type: Initial release