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 9SKD | pdb_00009skd

Model of M. pneumoniae 50S membrane complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

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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: 1,496.37 kDa 
  • Atom Count: 100,646 
  • Modeled Residue Count: 7,551 
  • Deposited Residue Count: 7,608 
  • Unique protein chains: 31
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34A [auth 0]47Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78006 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35B [auth 1]59Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75447 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36C [auth 2]37Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P52864 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
SecDFG [auth 9]944Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75387 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10H [auth A]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75240 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL12I [auth B],
J [auth C],
K [auth D],
L [auth E]		29Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75239 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2M [auth a]285Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75577 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3N [auth b]229Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75580 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4O [auth c]210Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75579 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5P [auth d]175Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50306 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6Q [auth e]176Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50303 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9R [auth f]145Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75540 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11S [auth h]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75550 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13T [auth i]144Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75178 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14U [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50308 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15V [auth k]148Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50300 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16W [auth l]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41204 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17X [auth m]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q59547 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18Y [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50302 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19Z [auth o]115Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75133 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20AA [auth p]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78023 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21BA [auth q]99Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78026 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22CA [auth r]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75575 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23DA [auth s]92Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75578 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24EA [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50307 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27FA [auth u]86Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75458 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28GA [auth v]63Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75171 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29HA [auth w]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50310 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31IA [auth x]44Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78020 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32JA [auth y]56Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75238 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AKA [auth z]50Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78015 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 4
MoleculeChains LengthOrganismImage
23S ribosomal RNAD [auth 3]2,878Mycoplasmoides pneumoniae M129
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S ribosomal RNAE [auth 4]105Mycoplasmoides pneumoniae M129
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Entity ID: 6
MoleculeChains LengthOrganismImage
tRNA-PheF [auth 8]51Mycoplasmoides pneumoniae M129
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 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