RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Gene Name = "b3936"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Escherichia coli (12)
	synthetic construct (9)
	Escherichia coli K-12 (5)
	Escherichia coli BL21 (2)
	Bacillus subtilis subsp. subtilis str. 168 (1)
	Capnocytophaga gingivalis (1)
	Escherichia coli 0.1197 (1)
	Thermus thermophilus HB8 (1)

Taxonomy

	Bacteria (16)
	other sequences (9)

Experimental Method

ELECTRON MICROSCOPY (16)

Polymer Entity Type

	Protein (16)
	RNA (16)
	DNA (9)

Refinement Resolution (Å)

	2.0 - 2.5 (2)
	2.5 - 3.0 (2)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)
	> 4.5 (7)

Release Date

	2005 - 2009 (1)
	2015 - 2019 (2)
	2020 - 2024 (9)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (1)

Symmetry Type

Asymmetric (16)

SCOP Classification

	Alpha and beta proteins (a+b) (1)
	All beta proteins (1)
	Alpha and beta proteins (a/b) (1)
	All alpha proteins (1)
	Small proteins (1)
	Peptides (1)

AllSelected

1 to 16 of 16 Structures

Page 1 of 1

Sort by

Explore in 3D

2J28 \| pdb_00002j28	Download File View File

MODEL OF E. COLI SRP BOUND TO 70S RNCS

Halic, M., Blau, M., Becker, T., Mielke, T., Pool, M.R., Wild, K., Sinning, I., Beckmann, R.

(2006) Nature 444: 508-511

Released	2006-11-08
Method	ELECTRON MICROSCOPY 9.5 Å
Organisms	Escherichia coli K-12
Macromolecule	Unique protein chains: 31 Unique nucleic acid chains: 3
Unique Ligands	MG

Explore in 3D

5MDY \| pdb_00005mdy	Download File View File

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)

James, N.R., Brown, A., Gordiyenko, Y., Ramakrishnan, V.

(2016) Science 354: 1437-1440

Released	2016-12-21
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	Escherichia coli Escherichia coli K-12 Thermus thermophilus HB8
Macromolecule	Unique protein chains: 53 Unique nucleic acid chains: 5
Unique Ligands	FME, MG, ZN

Explore in 3D

6SZS \| pdb_00006szs	Download File View File

Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis

Muller, C., Beckert, B., Wilson, D.N.

(2019) Nat Commun 10: 5397-5397

Released	2019-12-04
Method	ELECTRON MICROSCOPY 3.06 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 Escherichia coli K-12
Macromolecule	Unique protein chains: 51 Unique nucleic acid chains: 5

Explore in 3D

8UPO \| pdb_00008upo	Download File View File

Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 5.5 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 57 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8UPR \| pdb_00008upr	Download File View File

Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 5.3 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 58 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8UQL \| pdb_00008uql	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 58 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8UQM \| pdb_00008uqm	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 5.3 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 59 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8UQP \| pdb_00008uqp	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 58 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8UR0 \| pdb_00008ur0	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 59 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8URH \| pdb_00008urh	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 5.7 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 58 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8URI \| pdb_00008uri	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 5.3 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 59 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

8URX \| pdb_00008urx	Download File View File

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

Molodtsov, V., Wang, C., Ebright, R.H.

(2024) Nat Struct Mol Biol 31: 1932-1941

Released	2024-05-29
Method	ELECTRON MICROSCOPY 6.6 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Unique protein chains: 58 Unique nucleic acid chains: 7
Unique Ligands	MG, ZN

Explore in 3D

9MOR \| pdb_00009mor	Download File View File

Damaged 70S ribosome with PrfH bound

Tian, Y., Li, Q., Jin, H., Fatma, S., Zeng, F., Huang, R.H.

(2025) bioRxiv

Released	2025-02-05
Method	ELECTRON MICROSCOPY 2.65 Å
Organisms	Capnocytophaga gingivalis Escherichia coli
Macromolecule	Unique protein chains: 52 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

Explore in 3D

9MQ4 \| pdb_00009mq4	Download File View File

Damaged 70S ribosome with PrfH bound

Tian, Y., Li, Q., Jin, H., Fatma, S., Zeng, F., Huang, R.H.

(2025) bioRxiv

Released	2025-02-05
Method	ELECTRON MICROSCOPY 2.78 Å
Organisms	Escherichia coli Escherichia coli 0.1197
Macromolecule	Unique protein chains: 52 Unique nucleic acid chains: 5
Unique Ligands	MG, ZN

Explore in 3D

9N2B \| pdb_00009n2b	Download File View File

Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S)

Welfer, G.A., Brady, R.A., Natchiar, S.K., Watson, Z.L., Rundlet, E.J., Alejo, J.L., Singh, A.P., Mishra, N.K., Altman, R.B., Blanchard, S.C.

(2025) Philos Trans R Soc Lond B Biol Sci 380: 20230379-20230379

Released	2025-03-19
Method	ELECTRON MICROSCOPY 2.2 Å
Organisms	Escherichia coli BL21 Escherichia coli K-12
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 5
Unique Ligands	ATP, FME, K, MG, PUT, SPD, ZN

Explore in 3D

9N2C \| pdb_00009n2c	Download File View File

Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsH ribosome (HBB-70S)

Welfer, G.A., Brady, R.A., Natchiar, S.K., Watson, Z.L., Rundlet, E.J., Alejo, J.L., Singh, A.P., Mishra, N.K., Altman, R.B., Blanchard, S.C.

(2025) Philos Trans R Soc Lond B Biol Sci 380: 20230379-20230379

Released	2025-03-19
Method	ELECTRON MICROSCOPY 2.4 Å
Organisms	Escherichia coli BL21 Escherichia coli K-12
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 5
Unique Ligands	ATP, FME, K, MG, PUT, SPD, ZN

1 to 16 of 16 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

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.

2J28 | pdb_00002j28

MODEL OF E. COLI SRP BOUND TO 70S RNCS

5MDY | pdb_00005mdy

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)

6SZS | pdb_00006szs

Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis

8UPO | pdb_00008upo

Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8UPR | pdb_00008upr

Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8UQL | pdb_00008uql

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8UQM | pdb_00008uqm

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8UQP | pdb_00008uqp

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8UR0 | pdb_00008ur0

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8URH | pdb_00008urh

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8URI | pdb_00008uri

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

8URX | pdb_00008urx

Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome

9MOR | pdb_00009mor

Damaged 70S ribosome with PrfH bound

9MQ4 | pdb_00009mq4

Damaged 70S ribosome with PrfH bound

9N2B | pdb_00009n2b

Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsB ribosome (BBB-70S)

9N2C | pdb_00009n2c

Impacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsH ribosome (HBB-70S)

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2J28 | pdb_00002j28

5MDY | pdb_00005mdy

6SZS | pdb_00006szs

8UPO | pdb_00008upo

8UPR | pdb_00008upr

8UQL | pdb_00008uql

8UQM | pdb_00008uqm

8UQP | pdb_00008uqp

8UR0 | pdb_00008ur0

8URH | pdb_00008urh

8URI | pdb_00008uri

8URX | pdb_00008urx

9MOR | pdb_00009mor

9MQ4 | pdb_00009mq4

9N2B | pdb_00009n2b

9N2C | pdb_00009n2c