7QO4 | pdb_00007qo4

26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS)

PDB DOI: https://doi.org/10.2210/pdb7QO4/pdb
EM Map EMD-14083: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Saccharomyces cerevisiae, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-23 Released: 2022-06-01
Deposition Author(s): Hung, K.Y.S., Klumpe, S., Eisele, M.R., Elsasser, S., Geng, T.T., Cheng, C., Joshi, T., Rudack, T., Sakata, E., Finley, D.
Funding Organization(s): German Research Foundation (DFG), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.00 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

Allosteric control of Ubp6 and the proteasome via a bidirectional switch.

Hung, K.Y.S., Klumpe, S., Eisele, M.R., Elsasser, S., Tian, G., Sun, S., Moroco, J.A., Cheng, T.C., Joshi, T., Seibel, T., Van Dalen, D., Feng, X.H., Lu, Y., Ovaa, H., Engen, J.R., Lee, B.H., Rudack, T., Sakata, E., Finley, D.

(2022) Nat Commun 13: 838

DOI: https://doi.org/10.1038/s41467-022-28186-y

Macromolecule Content

Total Structure Weight: 470.51 kDa
Atom Count: 29,551
Modeled Residue Count: 3,737
Deposited Residue Count: 4,176
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN1	A [auth Z]	993	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38764 Go to UniProtKB: P38764
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38764
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT1 isoform 1	B [auth H]	467	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33299 Go to UniProtKB: P33299
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33299
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT2 isoform 1	C [auth I]	437	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40327 Go to UniProtKB: P40327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40327
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT3 isoform 1	D [auth K]	428	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33298 Go to UniProtKB: P33298
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33298
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT4 isoform 1	E [auth L]	437	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53549 Go to UniProtKB: P53549
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53549
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT5 isoform 1	F [auth M]	434	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33297 Go to UniProtKB: P33297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33297
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RPT6 isoform 1	G [auth J]	405	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01939 Go to UniProtKB: Q01939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01939
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase	H [auth 8]	499	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: UBP6, GI527_G0002094 EC: 3.4.19.12
UniProt
Find proteins for P43593 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43593 Go to UniProtKB: P43593
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43593
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	I [auth 9]	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain L [auth I] SDF format, chain N [auth K] SDF format, chain P [auth L] SDF format, chain R [auth M] MOL2 format, chain J [auth H] MOL2 format, chain L [auth I] MOL2 format, chain N [auth K] MOL2 format, chain P [auth L] MOL2 format, chain R [auth M] mmCIF format, chain J [auth H] mmCIF format, chain L [auth I] mmCIF format, chain N [auth K] mmCIF format, chain P [auth L] mmCIF format, chain R [auth M]	J [auth H], L [auth I], N [auth K], P [auth L], R [auth M]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth H] Focus chain L [auth I] Focus chain N [auth K] Focus chain P [auth L] Focus chain R [auth M] Interactions & Density Focus chain J [auth H] Focus chain L [auth I] Focus chain N [auth K] Focus chain P [auth L] Focus chain R [auth M]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain T [auth J] MOL2 format, chain T [auth J] mmCIF format, chain T [auth J]	T [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain T [auth J] Interactions & Density Focus chain T [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain M [auth I] SDF format, chain O [auth K] SDF format, chain Q [auth L] SDF format, chain S [auth M] SDF format, chain U [auth J] MOL2 format, chain K [auth H] MOL2 format, chain M [auth I] MOL2 format, chain O [auth K] MOL2 format, chain Q [auth L] MOL2 format, chain S [auth M] MOL2 format, chain U [auth J] mmCIF format, chain K [auth H] mmCIF format, chain M [auth I] mmCIF format, chain O [auth K] mmCIF format, chain Q [auth L] mmCIF format, chain S [auth M] mmCIF format, chain U [auth J]	K [auth H] M [auth I] O [auth K] Q [auth L] S [auth M] K [auth H], M [auth I], O [auth K], Q [auth L], S [auth M], U [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Focus chain M [auth I] Focus chain O [auth K] Focus chain Q [auth L] Focus chain S [auth M] Focus chain U [auth J] Interactions & Density Focus chain K [auth H] Focus chain M [auth I] Focus chain O [auth K] Focus chain Q [auth L] Focus chain S [auth M] Focus chain U [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GLZ Query on GLZ	I [auth 9]	L-PEPTIDE LINKING	C₂ H₅ N O		GLY

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 7.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2067/1- 390729940
German Research Foundation (DFG)	Germany	SFB1035/Project A01
German Research Foundation (DFG)	Germany	CRC889/Project A11
Other government		Foundation for the National Institutes of Health R01 GM043601
Other government		Marie Curie Career Integration grant (PCIG14-GA-2013-631577)

Revision History (Full details and data files)

Version 1.0: 2022-06-01
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.

7QO4 | pdb_00007qo4

26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS)

Literature

Allosteric control of Ubp6 and the proteasome via a bidirectional switch.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)