9CGC | pdb_00009cgc

Yeast 26S proteasome non-substrate-engaged (S1 state)

PDB DOI: https://doi.org/10.2210/pdb9CGC/pdb
EM Map EMD-45579: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2024-06-28 Released: 2025-07-09
Deposition Author(s): Arkinson, C., Gee, C.L., Martin, A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.61 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

Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome

Lopez-Alfonzo, E.M., Saurabh, A., Zarafshan, S., Gee, C.L., Arkinson, C., Presse, S., Martin, A.

To be published.

Macromolecule Content

Total Structure Weight: 1,479.58 kDa
Atom Count: 92,952
Modeled Residue Count: 11,779
Deposited Residue Count: 13,187
Unique protein chains: 32

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	A [auth 1], Z [auth b]	215	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38624
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	B [auth 2], EA [auth i]	261	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
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UniProt Group	P25043
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	C [auth 3], DA [auth h]	205	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
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UniProt Group	P25451
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	CA [auth g], D [auth 4]	198	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
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UniProt Group	P22141
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	BA [auth f], E [auth 5]	287	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30656
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	AA [auth e], F [auth 6]	241	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
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UniProt Group	P23724
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	G [auth 7], Y [auth a]	266	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
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UniProt Group	P30657
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	H [auth A]	252	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21243
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	I [auth B]	250	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
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UniProt Group	P23639
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	J [auth C]	258	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
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UniProt Group	P23638
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	K [auth D]	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
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UniProt Group	P40303
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	L [auth E]	260	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
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UniProt Group	P32379
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	M [auth F]	234	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40302
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	N [auth G]	288	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
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UniProt Group	P21242
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 4 homolog	O [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
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UniProt Group	P40327
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6B homolog	P [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
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UniProt Group	P33298
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome subunit RPT4	Q [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
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UniProt Group	P53549
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN9	R [auth O]	393	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04062 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04062 Go to UniProtKB: Q04062
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UniProt Group	Q04062
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN5	S [auth P]	445	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12250 Go to UniProtKB: Q12250
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UniProt Group	Q12250
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN7	T [auth R]	429	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06103 Go to UniProtKB: Q06103
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UniProt Group	Q06103
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN3	U [auth S]	523	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40016 Go to UniProtKB: P40016
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UniProt Group	P40016
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase RPN11	V	306	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43588 Go to UniProtKB: P43588
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UniProt Group	P43588
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN10	W	268	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38886 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38886 Go to UniProtKB: P38886
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UniProt Group	P38886
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	X [auth Y]	89	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O94742 Go to UniProtKB: O94742
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UniProt Group	O94742
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 8 homolog	FA [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
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UniProt Group	Q01939
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 7 homolog	GA [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
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UniProt Group	P33299
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6A	HA [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
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UniProt Group	P33297
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN6	IA [auth Q]	434	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12377 Go to UniProtKB: Q12377
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UniProt Group	Q12377
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN8	JA [auth U]	338	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08723 Go to UniProtKB: Q08723
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UniProt Group	Q08723
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN2	KA [auth N]	945	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32565 Go to UniProtKB: P32565
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UniProt Group	P32565
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN12	LA [auth T]	274	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32496 Go to UniProtKB: P32496
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UniProt Group	P32496
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN1	MA [auth o]	993	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38764 Go to UniProtKB: P38764
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UniProt Group	P38764
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Reference Sequence

Small Molecules

Ligands 4 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 OA [auth K] SDF format, chain QA [auth L] SDF format, chain TA [auth J] SDF format, chain VA [auth H] SDF format, chain XA [auth M] MOL2 format, chain OA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain TA [auth J] MOL2 format, chain VA [auth H] MOL2 format, chain XA [auth M] mmCIF format, chain OA [auth K] mmCIF format, chain QA [auth L] mmCIF format, chain TA [auth J] mmCIF format, chain VA [auth H] mmCIF format, chain XA [auth M]	OA [auth K], QA [auth L], TA [auth J], VA [auth H], XA [auth M]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain OA [auth K] Focus chain QA [auth L] Focus chain TA [auth J] Focus chain VA [auth H] Focus chain XA [auth M] Interactions & Density Focus chain OA [auth K] Focus chain QA [auth L] Focus chain TA [auth J] Focus chain VA [auth H] Focus chain XA [auth M]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain UA [auth J] MOL2 format, chain UA [auth J] mmCIF format, chain UA [auth J]	UA [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain UA [auth J] Interactions & Density Focus chain UA [auth J]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain SA [auth V] MOL2 format, chain SA [auth V] mmCIF format, chain SA [auth V]	SA [auth V]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain SA [auth V] Interactions & Density Focus chain SA [auth V]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain WA [auth H] SDF format, chain YA [auth M] SDF format, chain RA [auth L] SDF format, chain PA [auth K] SDF format, chain NA [auth I] MOL2 format, chain WA [auth H] MOL2 format, chain YA [auth M] MOL2 format, chain RA [auth L] MOL2 format, chain PA [auth K] MOL2 format, chain NA [auth I] mmCIF format, chain WA [auth H] mmCIF format, chain YA [auth M] mmCIF format, chain RA [auth L] mmCIF format, chain PA [auth K] mmCIF format, chain NA [auth I]	NA [auth I], PA [auth K], RA [auth L], WA [auth H], YA [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain NA [auth I] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain WA [auth H] Focus chain YA [auth M] Interactions & Density Focus chain NA [auth I] Focus chain PA [auth K] Focus chain RA [auth L] Focus chain WA [auth H] Focus chain YA [auth M]