9SKE | pdb_00009ske

Model of M. pneumoniae 50S RRF EF-G

PDB DOI: https://doi.org/10.2210/pdb9SKE/pdb
EM Map EMD-53627: EMDB EMDataResource

Classification: TRANSLATION
Organism(s): Mycoplasmoides pneumoniae M129
Mutation(s): No

Deposited: 2025-09-02 Released: 2026-09-23
Deposition Author(s): Dobbs, J.M., Mahamid, J.
Funding Organization(s): Chan Zuckerberg Initiative, Independent Research Fund Denmark - Medical Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: CELL
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

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: 1,541.08 kDa
Atom Count: 100,914
Modeled Residue Count: 7,580
Deposited Residue Count: 7,938
Unique protein chains: 32
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	A [auth 0]	47	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78006 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78006 Go to UniProtKB: P78006
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78006
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	B [auth 1]	59	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75447 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75447 Go to UniProtKB: P75447
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75447
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	C [auth 2]	37	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P52864 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P52864 Go to UniProtKB: P52864
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52864
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-recycling factor	F [auth 7]	184	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75161 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75161 Go to UniProtKB: P75161
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75161
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor G	H [auth A]	675	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75544 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75544 Go to UniProtKB: P75544
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75544
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7/L12	I [auth B], J [auth C], K [auth D], L [auth E]	122	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75239 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75239 Go to UniProtKB: P75239
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75239
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	M [auth F]	161	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75240 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75240 Go to UniProtKB: P75240
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75240
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	N [auth a]	285	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75577 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75577 Go to UniProtKB: P75577
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75577
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	O [auth b]	229	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75580 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75580 Go to UniProtKB: P75580
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75580
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	P [auth c]	210	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75579 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75579 Go to UniProtKB: P75579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75579
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	Q [auth d]	175	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50306 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50306 Go to UniProtKB: Q50306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50306
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	R [auth e]	176	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50303 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50303 Go to UniProtKB: Q50303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50303
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	S [auth f]	145	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75540 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75540 Go to UniProtKB: P75540
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75540
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL11	T [auth h]	128	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75550 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75550 Go to UniProtKB: P75550
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75550
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	U [auth i]	144	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75178 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75178 Go to UniProtKB: P75178
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75178
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	V [auth j]	122	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50308 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50308 Go to UniProtKB: Q50308
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50308
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	W [auth k]	148	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50300 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50300 Go to UniProtKB: Q50300
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50300
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	X [auth l]	136	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P41204 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P41204 Go to UniProtKB: P41204
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41204
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	Y [auth m]	119	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q59547 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q59547 Go to UniProtKB: Q59547
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59547
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	Z [auth n]	116	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50302 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50302 Go to UniProtKB: Q50302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50302
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	AA [auth o]	115	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75133 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75133 Go to UniProtKB: P75133
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75133
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	BA [auth p]	114	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78023 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78023 Go to UniProtKB: P78023
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78023
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	CA [auth q]	99	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78026 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78026 Go to UniProtKB: P78026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78026
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Reference Sequence

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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	DA [auth r]	139	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75575 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75575 Go to UniProtKB: P75575
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75575
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	EA [auth s]	92	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75578 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75578 Go to UniProtKB: P75578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75578
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Reference Sequence

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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	FA [auth t]	111	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50307 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50307 Go to UniProtKB: Q50307
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50307
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	GA [auth u]	86	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75458 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75458 Go to UniProtKB: P75458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75458
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	HA [auth v]	63	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75171 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75171 Go to UniProtKB: P75171
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75171
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	IA [auth w]	108	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for Q50310 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore Q50310 Go to UniProtKB: Q50310
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50310
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL31	JA [auth x]	44	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78020 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78020 Go to UniProtKB: P78020
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78020
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	KA [auth y]	56	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P75238 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75238 Go to UniProtKB: P75238
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75238
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33A	LA [auth z]	50	Mycoplasmoides pneumoniae M129	Mutation(s): 0
UniProt
Find proteins for P78015 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P78015 Go to UniProtKB: P78015
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78015
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
23S ribosomal RNA	D [auth 3]	2,893	Mycoplasmoides pneumoniae M129
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
5S ribosomal RNA	E [auth 4]	108	Mycoplasmoides pneumoniae M129
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Molecule	Chains	Length	Organism
Entity ID: 7
tRNA-Phe	G [auth 8]	76	Mycoplasmoides pneumoniae M129
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: CELL
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
RECONSTRUCTION	M

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Dobbs, J.M.

Mahamid, J.

Funding Organization	Location	Grant Number
Chan Zuckerberg Initiative	United States	2021-234620
Independent Research Fund Denmark - Medical Sciences	Denmark	0106-00010A

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9SKE | pdb_00009ske

Model of M. pneumoniae 50S RRF EF-G

Literature

Visual proteomics of translational control in a minimal bacterium

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

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Sequence Annotations

Entity ID: 3

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Entity ID: 6

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

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Entity ID: 20

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Entity ID: 21

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Entity ID: 22

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