8A5Y

S. cerevisiae apo unphosphorylated APC/C.

PDB DOI: https://doi.org/10.2210/pdb8A5Y/pdb
EM Map EMD-15199: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Saccharomyces cerevisiae
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-06-16 Released: 2022-08-31
Deposition Author(s): Barford, D., Fernandez-Vazquez, E., Zhang, Z., Yang, J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structure of the S. cerevisiae APC/C-Cdh1 complex and comparison to apo unphosphorylated and phosphorylated states

Barford, D., Fernandez-Vazquez, E., Zhang, Z., Yang, J.

To be published.

Macromolecule Content

Total Structure Weight: 1,130.36 kDa
Atom Count: 57,866
Modelled Residue Count: 7,213
Deposited Residue Count: 9,872
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC27	A [auth F], F [auth H]	758	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC27, APC3, SNB1, YBL084C, YBL0718
UniProt
Find proteins for P38042 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38042 Go to UniProtKB: P38042
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38042
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC16	B [auth J], C [auth K]	850	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC16, YKL022C
UniProt
Find proteins for P09798 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09798 Go to UniProtKB: P09798
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UniProt Group	P09798
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC26	D [auth G], E [auth W]	124	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC26, HIT3, SCD26, YFR036W
UniProt
Find proteins for P14724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14724 Go to UniProtKB: P14724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14724
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 9	G [auth E]	265	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC9, YLR102C
UniProt
Find proteins for Q12107 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12107 Go to UniProtKB: Q12107
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UniProt Group	Q12107
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 2	H [auth T]	853	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC2, RSI1, YLR127C, L3105, L3108
UniProt
Find proteins for Q12440 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12440 Go to UniProtKB: Q12440
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UniProt Group	Q12440
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 11	I [auth U]	165	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC11, YDL008W, D2900 EC: 6.3.2
UniProt
Find proteins for Q12157 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12157 Go to UniProtKB: Q12157
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UniProt Group	Q12157
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 1	J [auth C]	1,748	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC1, YNL172W, N1677
UniProt
Find proteins for P53886 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53886 Go to UniProtKB: P53886
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UniProt Group	P53886
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 5	K [auth O]	685	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC5, RMC1, YOR249C
UniProt
Find proteins for Q08683 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08683 Go to UniProtKB: Q08683
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UniProt Group	Q08683
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC23	L [auth D], M [auth P]	626	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC23, YHR166C
UniProt
Find proteins for P16522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16522 Go to UniProtKB: P16522
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UniProt Group	P16522
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit SWM1	N [auth I]	170	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SWM1, APC13, YDR260C, YD9320A.11, YD9320A.11c
UniProt
Find proteins for Q12379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12379 Go to UniProtKB: Q12379
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12379
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit MND2	O [auth N]	368	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MND2, YIR025W
UniProt
Find proteins for P40577 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40577 Go to UniProtKB: P40577
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UniProt Group	P40577
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 4	P [auth Q]	652	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: APC4, YDR118W
UniProt
Find proteins for Q04601 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04601 Go to UniProtKB: Q04601
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UniProt Group	Q04601
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit DOC1	Q [auth A]	250	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DOC1, APC10, YGL240W, HRC283
UniProt
Find proteins for P53068 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53068 Go to UniProtKB: P53068
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UniProt Group	P53068
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain R [auth U] SDF format, chain S [auth U] SDF format, chain T [auth U] MOL2 format, chain R [auth U] MOL2 format, chain S [auth U] MOL2 format, chain T [auth U]	R [auth U], S [auth U], T [auth U]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth U] Focus chain S [auth U] Focus chain T [auth U] Interactions & Density Focus chain R [auth U] Focus chain S [auth U] Focus chain T [auth U]