9E1S | pdb_00009e1s

Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit

PDB DOI: https://doi.org/10.2210/pdb9E1S/pdb
EM Map EMD-47419: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Mycobacterium tuberculosis
Mutation(s): No

Deposited: 2024-10-21 Released: 2026-09-02
Deposition Author(s): Majumdar, S., Ojha, A.K., Agrawal, R.K.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

DOI: https://doi.org/10.1101/2024.11.25.625233

Macromolecule Content

Total Structure Weight: 1,466.7 kDa
Atom Count: 94,689
Modeled Residue Count: 6,490
Deposited Residue Count: 7,008
Unique protein chains: 30
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein bL37	A [auth 7]	24	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal tunnel occlusion factor-RTOF	C [auth 1]	62	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	D [auth 0]	57	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IMI5 (Mycobacterium tuberculosis) Explore A0A045IMI5 Go to UniProtKB: A0A045IMI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IMI5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein bL34	E [auth 2]	47	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	F [auth 3]	64	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045KKY9 (Mycobacterium tuberculosis) Explore A0A045KKY9 Go to UniProtKB: A0A045KKY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045KKY9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein bL36	G [auth 4]	37	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	I [auth C]	280	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045H5T7 (Mycobacterium tuberculosis) Explore A0A045H5T7 Go to UniProtKB: A0A045H5T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045H5T7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	J [auth D]	217	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045HU18 (Mycobacterium tuberculosis) Explore A0A045HU18 Go to UniProtKB: A0A045HU18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045HU18
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	K [auth E]	223	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045J9H1 (Mycobacterium tuberculosis) Explore A0A045J9H1 Go to UniProtKB: A0A045J9H1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045J9H1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	L [auth F]	187	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045HUU0 (Mycobacterium tuberculosis) Explore A0A045HUU0 Go to UniProtKB: A0A045HUU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045HUU0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	M [auth G]	179	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045JJU1 (Mycobacterium tuberculosis) Explore A0A045JJU1 Go to UniProtKB: A0A045JJU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045JJU1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	N [auth H]	152	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045JW48 (Mycobacterium tuberculosis) Explore A0A045JW48 Go to UniProtKB: A0A045JW48
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045JW48
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	O [auth J]	195	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis) Explore A0A0T9D5H2 Go to UniProtKB: A0A0T9D5H2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0T9D5H2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	P [auth K]	122	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for P66070 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)) Explore P66070 Go to UniProtKB: P66070
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P66070
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	Q [auth L]	146	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IWY0 (Mycobacterium tuberculosis) Explore A0A045IWY0 Go to UniProtKB: A0A045IWY0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IWY0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	R [auth M]	138	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IWV9 (Mycobacterium tuberculosis) Explore A0A045IWV9 Go to UniProtKB: A0A045IWV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IWV9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	S [auth N]	180	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IVA2 (Mycobacterium tuberculosis) Explore A0A045IVA2 Go to UniProtKB: A0A045IVA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IVA2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	T [auth O]	122	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045JK28 (Mycobacterium tuberculosis) Explore A0A045JK28 Go to UniProtKB: A0A045JK28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045JK28
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	U [auth P]	113	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IDD2 (Mycobacterium tuberculosis) Explore A0A045IDD2 Go to UniProtKB: A0A045IDD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IDD2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	V [auth Q]	129	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045KJ85 (Mycobacterium tuberculosis) Explore A0A045KJ85 Go to UniProtKB: A0A045KJ85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045KJ85
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	W [auth R]	104	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A2I7W9M4 (Mycobacterium tuberculosis) Explore A0A2I7W9M4 Go to UniProtKB: A0A2I7W9M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I7W9M4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	X [auth S]	197	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045H760 (Mycobacterium tuberculosis) Explore A0A045H760 Go to UniProtKB: A0A045H760
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045H760
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	Y [auth T]	100	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045J9M3 (Mycobacterium tuberculosis) Explore A0A045J9M3 Go to UniProtKB: A0A045J9M3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045J9M3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	Z [auth V]	215	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045JAK4 (Mycobacterium tuberculosis) Explore A0A045JAK4 Go to UniProtKB: A0A045JAK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045JAK4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	AA [auth W]	86	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045K0G1 (Mycobacterium tuberculosis) Explore A0A045K0G1 Go to UniProtKB: A0A045K0G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045K0G1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	BA [auth Y]	77	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IQ64 (Mycobacterium tuberculosis) Explore A0A045IQ64 Go to UniProtKB: A0A045IQ64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IQ64
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	CA [auth Z]	65	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045H4J2 (Mycobacterium tuberculosis) Explore A0A045H4J2 Go to UniProtKB: A0A045H4J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045H4J2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein bL33-c minus	DA [auth b]	54	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein bL28-c minus	EA [auth y]	78	Mycobacterium tuberculosis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein uL24	FA [auth U]	105	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for A0A045IXU4 (Mycobacterium tuberculosis) Explore A0A045IXU4 Go to UniProtKB: A0A045IXU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A045IXU4
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
23S ribosomal RNA	B [auth I]	3,138	Mycobacterium tuberculosis
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 8
5S ribosomal RNA	H [auth B]	115	Mycobacterium tuberculosis
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.4.0
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Majumdar, S.

Ojha, A.K.

Agrawal, R.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI32422

Revision History (Full details and data files)

Version 1.0: 2026-09-02
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.

9E1S | pdb_00009e1s

Cryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit

Literature

A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity Groups

Sequence Annotations

Entity ID: 3

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations

Entity ID: 20

UniProt

Entity Groups

Sequence Annotations

Entity ID: 21

UniProt

Entity Groups

Sequence Annotations

Entity ID: 22

UniProt