28YE | pdb_000028ye

50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi

PDB DOI: https://doi.org/10.2210/pdb28YE/pdb
EM Map EMD-56961: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Asaia platycodi JCM 25414
Mutation(s): No

Deposited: 2026-02-27 Released: 2026-06-03
Deposition Author(s): Chan, L.I., Omae, K., Amikura, K., Suzuki, S., Melnikov, S.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Royal Society, Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The Evolutionary Lifecycle of Ribosome Hibernation Factors

Chan, L.I., Melnikov, S.V.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.11.04.686544v2.full

Macromolecule Content

Total Structure Weight: 1,307.08 kDa
Atom Count: 79,050
Modeled Residue Count: 5,708
Deposited Residue Count: 6,339
Unique protein chains: 27
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL36	A [auth Z]	41	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	B [auth A]	276	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	D [auth C]	67	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	E [auth D]	44	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	F [auth E]	55	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	G [auth F]	67	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	H	61	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	I	77	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	J	100	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	K	88	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	L	212	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	M	106	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	N	113	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	O	143	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	P	104	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	Q	128	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	R [auth S]	141	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	S [auth T]	138	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	T [auth U]	161	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	U [auth V]	122	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	V [auth W]	158	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	W [auth X]	192	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	X [auth Y]	178	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	Y [auth a]	204	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	Z [auth b]	227	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	CA [auth R]	127	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome silencing factor S	DA [auth G]	152	Asaia platycodi JCM 25414	Mutation(s): 0

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
23S rRNA	C [auth B]	2,726	Asaia platycodi JCM 25414
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 27
E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)	AA [auth c]	18	Asaia platycodi JCM 25414
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 28
5S rRNA (fragment)	BA [auth d]	113	Asaia platycodi JCM 25414
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	5.0.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T008695/1
Royal Society	United Kingdom	ICA/R2/242249
Japan Science and Technology	Japan	JPMJCR20S4

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.

28YE | pdb_000028ye

50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi

Literature

The Evolutionary Lifecycle of Ribosome Hibernation Factors

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity ID: 2

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7

Entity ID: 8

Entity ID: 9

Entity ID: 10

Entity ID: 11

Entity ID: 12

Entity ID: 13

Entity ID: 14

Entity ID: 15

Entity ID: 16

Entity ID: 17

Entity ID: 18

Entity ID: 19

Entity ID: 20

Entity ID: 21

Entity ID: 22

Entity ID: 23

Entity ID: 24

Entity ID: 25

Entity ID: 26

Entity ID: 29

Entity ID: 30

Entity ID: 3

Sequence Annotations

Expand

Entity ID: 27

Sequence Annotations

Expand

Entity ID: 28

Sequence Annotations

Expand

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)