Macromolecule Content

Total Structure Weight: 1,663.45 kDa
Atom Count: 99,911
Modelled Residue Count: 12,865
Deposited Residue Count: 14,855
Unique protein chains: 32

7QY7

Proteasome-ZFAND5 Complex Z-A state

PDB DOI: 10.2210/pdb7QY7/pdb
EM Map EMD-14209: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2022-01-27 Released: 2023-02-08
Deposition Author(s): Zhu, Y., Lu, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.70 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

Mechanism of 26S proteasome activation by the 19S-interacting protein ZFAND5

Zhu, Y., Lu, Y.

To be published.

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 13	A [auth a]	376	Homo sapiens	Mutation(s): 0 Gene Names: PSMD13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNM6 (Homo sapiens) Explore Q9UNM6 Go to UniProtKB: Q9UNM6
PHAROS: Q9UNM6
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UniProt Group	Q9UNM6
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	B [auth b]	377	Homo sapiens	Mutation(s): 0 Gene Names: PSMD4, MCB1
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Find proteins for P55036 (Homo sapiens) Explore P55036 Go to UniProtKB: P55036
PHAROS: P55036
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55036
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 14	C [auth c]	309	Homo sapiens	Mutation(s): 0 Gene Names: PSMD14, POH1 EC: 3.4.19
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Find proteins for O00487 (Homo sapiens) Explore O00487 Go to UniProtKB: O00487
PHAROS: O00487
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00487
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 8	D [auth d]	349	Homo sapiens	Mutation(s): 0 Gene Names: PSMD8
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Find proteins for P48556 (Homo sapiens) Explore P48556 Go to UniProtKB: P48556
PHAROS: P48556
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48556
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	E [auth e]	70	Homo sapiens	Mutation(s): 0 Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
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Find proteins for P60896 (Homo sapiens) Explore P60896 Go to UniProtKB: P60896
PHAROS: P60896
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60896
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 2	F [auth f]	908	Homo sapiens	Mutation(s): 0 Gene Names: PSMD2, TRAP2
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Find proteins for Q13200 (Homo sapiens) Explore Q13200 Go to UniProtKB: Q13200
PHAROS: Q13200
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13200
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 1	G [auth U]	953	Homo sapiens	Mutation(s): 0 Gene Names: PSMD1
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Find proteins for Q99460 (Homo sapiens) Explore Q99460 Go to UniProtKB: Q99460
PHAROS: Q99460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99460
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 3	H [auth V]	533	Homo sapiens	Mutation(s): 0 Gene Names: PSMD3
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Find proteins for O43242 (Homo sapiens) Explore O43242 Go to UniProtKB: O43242
PHAROS: O43242
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43242
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 12	I [auth W]	456	Homo sapiens	Mutation(s): 0 Gene Names: PSMD12
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Find proteins for O00232 (Homo sapiens) Explore O00232 Go to UniProtKB: O00232
PHAROS: O00232
Entity Groups
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UniProt Group	O00232
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 11	J [auth X]	422	Homo sapiens	Mutation(s): 0 Gene Names: PSMD11
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Find proteins for O00231 (Homo sapiens) Explore O00231 Go to UniProtKB: O00231
PHAROS: O00231
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UniProt Group	O00231
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 6	K [auth Y]	389	Homo sapiens	Mutation(s): 0 Gene Names: PSMD6, KIAA0107, PFAAP4
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Find proteins for Q15008 (Homo sapiens) Explore Q15008 Go to UniProtKB: Q15008
PHAROS: Q15008
Entity Groups
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UniProt Group	Q15008
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 7	L [auth Z]	324	Homo sapiens	Mutation(s): 0 Gene Names: PSMD7, MOV34L
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Find proteins for P51665 (Homo sapiens) Explore P51665 Go to UniProtKB: P51665
PHAROS: P51665
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51665
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 7	M [auth A]	433	Homo sapiens	Mutation(s): 0 Gene Names: PSMC2, MSS1
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Find proteins for P35998 (Homo sapiens) Explore P35998 Go to UniProtKB: P35998
PHAROS: P35998
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35998
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 4	N [auth B]	440	Homo sapiens	Mutation(s): 0 Gene Names: PSMC1
UniProt
Find proteins for P62191 (Homo sapiens) Explore P62191 Go to UniProtKB: P62191
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UniProt Group	P62191
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
PSMC5 isoform 15	O [auth C]	394	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A6D2XG74 (Pongo abelii) Explore A0A6D2XG74 Go to UniProtKB: A0A6D2XG74
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UniProt Group	A0A6D2XG74
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6B	P [auth D]	418	Homo sapiens	Mutation(s): 0 Gene Names: PSMC4, MIP224, TBP7
UniProt & NIH Common Fund Data Resources
Find proteins for P43686 (Homo sapiens) Explore P43686 Go to UniProtKB: P43686
PHAROS: P43686
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43686
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 10B	Q [auth E]	403	Homo sapiens	Mutation(s): 0 Gene Names: PSMC6
UniProt
Find proteins for A0A087X2I1 (Homo sapiens) Explore A0A087X2I1 Go to UniProtKB: A0A087X2I1
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A087X2I1
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6A	R [auth F]	439	Homo sapiens	Mutation(s): 0 Gene Names: PSMC3, TBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P17980 (Homo sapiens) Explore P17980 Go to UniProtKB: P17980
PHAROS: P17980
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17980
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	S [auth G], GA [auth g]	245	Homo sapiens	Mutation(s): 0 Gene Names: PSMA6, PROS27
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Find proteins for P60900 (Homo sapiens) Explore P60900 Go to UniProtKB: P60900
PHAROS: P60900
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60900
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	T [auth H], HA [auth h]	233	Homo sapiens	Mutation(s): 0 Gene Names: PSMA2, HC3, PSC3
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Find proteins for P25787 (Homo sapiens) Explore P25787 Go to UniProtKB: P25787
PHAROS: P25787
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25787
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	U [auth I], IA [auth i]	260	Homo sapiens	Mutation(s): 0 Gene Names: PSMA4, HC9, PSC9
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Find proteins for P25789 (Homo sapiens) Explore P25789 Go to UniProtKB: P25789
PHAROS: P25789
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25789
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	V [auth J], JA [auth j]	247	Homo sapiens	Mutation(s): 0 Gene Names: PSMA7, HSPC
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Find proteins for O14818 (Homo sapiens) Explore O14818 Go to UniProtKB: O14818
PHAROS: O14818
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14818
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	W [auth K], KA [auth k]	240	Homo sapiens	Mutation(s): 0 Gene Names: PSMA5
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Find proteins for P28066 (Homo sapiens) Explore P28066 Go to UniProtKB: P28066
PHAROS: P28066
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28066
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Long of Proteasome subunit alpha type-1	X [auth L], LA [auth l]	268	Homo sapiens	Mutation(s): 0 Gene Names: PSMA1, HC2, NU, PROS30, PSC2
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Explore P25786 Go to UniProtKB: P25786
PHAROS: P25786
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25786
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	Y [auth M], MA [auth m]	254	Homo sapiens	Mutation(s): 0 Gene Names: PSMA3, HC8, PSC8
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Find proteins for P25788 (Homo sapiens) Explore P25788 Go to UniProtKB: P25788
PHAROS: P25788
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25788
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	Z [auth N], NA [auth n]	238	Homo sapiens	Mutation(s): 0 Gene Names: PSMB6, LMPY, Y EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens) Explore P28072 Go to UniProtKB: P28072
PHAROS: P28072
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28072
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	AA [auth O], OA [auth o]	276	Homo sapiens	Mutation(s): 0 Gene Names: PSMB7, Z EC: 3.4.25.1
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Find proteins for Q99436 (Homo sapiens) Explore Q99436 Go to UniProtKB: Q99436
PHAROS: Q99436
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99436
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	BA [auth P], PA [auth p]	204	Homo sapiens	Mutation(s): 0 Gene Names: PSMB3 EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens) Explore P49720 Go to UniProtKB: P49720
PHAROS: P49720
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UniProt Group	P49720
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	CA [auth Q], QA [auth q]	201	Homo sapiens	Mutation(s): 0 Gene Names: PSMB2 EC: 3.4.25.1
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Find proteins for P49721 (Homo sapiens) Explore P49721 Go to UniProtKB: P49721
PHAROS: P49721
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49721
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	DA [auth R], RA [auth r]	262	Homo sapiens	Mutation(s): 0 Gene Names: PSMB5, LMPX, MB1, X EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens) Explore P28074 Go to UniProtKB: P28074
PHAROS: P28074
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28074
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	EA [auth S], SA [auth s]	240	Homo sapiens	Mutation(s): 0 Gene Names: PSMB1, PSC5
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Find proteins for P20618 (Homo sapiens) Explore P20618 Go to UniProtKB: P20618
PHAROS: P20618
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20618
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	FA [auth T], TA [auth t]	263	Homo sapiens	Mutation(s): 0 Gene Names: PSMB4, PROS26
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Find proteins for P28070 (Homo sapiens) Explore P28070 Go to UniProtKB: P28070
PHAROS: P28070
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28070
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain VA [auth A] SDF format, chain WA [auth B] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth E] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth E]	VA [auth A], WA [auth B], XA [auth D], YA [auth D], ZA [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Ligand Interaction
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain UA [auth c] MOL2 format, chain UA [auth c]	UA [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Zhu, Y.

Lu, Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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Help and Resources

7QY7

Proteasome-ZFAND5 Complex Z-A state

Mechanism of 26S proteasome activation by the 19S-interacting protein ZFAND5

Entity ID: 1

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19