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: Enzyme Classification Number = 2.1.1.310

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 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Saccharomyces cerevisiae BY4741 (8)
	Saccharomyces cerevisiae S288C (3)
	Saccharomyces cerevisiae (1)
	Saccharomyces cerevisiae BY4741-AV16 (1)

Taxonomy

Eukaryota (11)

Experimental Method

ELECTRON MICROSCOPY (11)

Polymer Entity Type

	Protein (11)
	RNA (11)

Refinement Resolution (Å)

	2.5 - 3.0 (3)
	3.0 - 3.5 (5)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (9)

Enzyme Classification Name

	Transferases (11)
	Hydrolases (8)

Symmetry Type

Asymmetric (11)

AllSelected

1 to 11 of 11 Structures

Page 1 of 1

Sort by

Explore in 3D

6ELZ \| pdb_00006elz	Download File View File

State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

Kater, L., Cheng, J., Barrio-Garcia, C., Hurt, E., Beckmann, R.

(2017) Cell 171: 1599-1610.e14

Released	2017-12-27
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 51 Unique nucleic acid chains: 3
Unique Ligands	ZN

Explore in 3D

6EM5 \| pdb_00006em5	Download File View File

State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

Kater, L., Cheng, J., Barrio-Garcia, C., Hurt, E., Beckmann, R.

(2017) Cell 171: 1599-1610.e14

Released	2017-12-27
Method	ELECTRON MICROSCOPY 4.3 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 3

Explore in 3D

7NAC \| pdb_00007nac	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 55 Unique nucleic acid chains: 3
Unique Ligands	SAH, ZN

Explore in 3D

7NAF \| pdb_00007naf	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.13 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 1
Unique Ligands	SAH

Explore in 3D

7OHR \| pdb_00007ohr	Download File View File

Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae

Milkereit, P., Poell, G.

(2021) PLoS One 16: e0252497-e0252497

Released	2021-11-10
Method	ELECTRON MICROSCOPY 4.72 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 48 Unique nucleic acid chains: 3
Unique Ligands	ZN

Explore in 3D

7R6K \| pdb_00007r6k	Download File View File

State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.17 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 1

Explore in 3D

7R7A \| pdb_00007r7a	Download File View File

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 54 Unique nucleic acid chains: 3
Unique Ligands	ZN

Explore in 3D

7R7C \| pdb_00007r7c	Download File View File

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model

Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

(2022) Nat Struct Mol Biol 29: 1228-1238

Released	2022-11-09
Method	ELECTRON MICROSCOPY 3.71 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 10 Unique nucleic acid chains: 1

Explore in 3D

8V83 \| pdb_00008v83	Download File View File

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.53 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 45 Unique nucleic acid chains: 3
Unique Ligands	ZN

Explore in 3D

8V84 \| pdb_00008v84	Download File View File

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Saccharomyces cerevisiae BY4741 Saccharomyces cerevisiae BY4741-AV16
Macromolecule	Unique protein chains: 46 Unique nucleic acid chains: 3
Unique Ligands	GDP, MG, ZN

Explore in 3D

8V87 \| pdb_00008v87	Download File View File

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)

Cruz, V.E., Weirich, C.S., Peddada, N., Erzberger, J.P.

(2024) Nat Commun 15: 3296-3296

Released	2024-05-01
Method	ELECTRON MICROSCOPY 2.66 Å
Organisms	Saccharomyces cerevisiae BY4741
Macromolecule	Unique protein chains: 53 Unique nucleic acid chains: 3
Unique Ligands	ADP, GDP, K, MG, ZN

1 to 11 of 11 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.

6ELZ | pdb_00006elz

State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

6EM5 | pdb_00006em5

State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

7NAC | pdb_00007nac

State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model

7NAF | pdb_00007naf

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model

7OHR | pdb_00007ohr

Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae

7R6K | pdb_00007r6k

State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region

7R7A | pdb_00007r7a

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

7R7C | pdb_00007r7c

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model

8V83 | pdb_00008v83

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

8V84 | pdb_00008v84

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)

8V87 | pdb_00008v87

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)

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

6ELZ | pdb_00006elz

6EM5 | pdb_00006em5

7NAC | pdb_00007nac

7NAF | pdb_00007naf

7OHR | pdb_00007ohr

7R6K | pdb_00007r6k

7R7A | pdb_00007r7a

7R7C | pdb_00007r7c

8V83 | pdb_00008v83

8V84 | pdb_00008v84

8V87 | pdb_00008v87