8A3T | pdb_00008a3t

S. cerevisiae APC/C-Cdh1 complex

PDB DOI: https://doi.org/10.2210/pdb8A3T/pdb
EM Map EMD-15123: EMDB EMDataResource

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

Deposited: 2022-06-09 Released: 2022-08-31
Deposition Author(s): Barford, D., Vazquez-Fernandez, E., Zhang, Z., Yang, J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the S. cerevisiae APC/C-Cdh1 complex

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

To be published.

Macromolecule Content

Total Structure Weight: 1,363.12 kDa
Atom Count: 61,351
Modeled Residue Count: 7,661
Deposited Residue Count: 11,956
Unique protein chains: 15

Macromolecules

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38042
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09798
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14724
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12107
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit DOC1	H [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53068
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CDH1 isoform 1	I [auth B]	566	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDH1, GI527_G0002420
UniProt
Find proteins for P53197 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53197 Go to UniProtKB: P53197
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53197
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
HSL1 isoform 1	J [auth S]	1,518	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: HSL1, GI527_G0003535 EC: 2.7.11.1
UniProt
Find proteins for P34244 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34244 Go to UniProtKB: P34244
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34244
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 1	K [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53886
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 5	L [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08683
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC23	M [auth D], N [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16522
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit SWM1	O [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12379
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit MND2	P [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40577
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 4	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04601
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 2	R [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12440
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Reference Sequence

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 11	S [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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12157
Sequence Annotations Expand
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 T [auth U] SDF format, chain U SDF format, chain V [auth U] MOL2 format, chain T [auth U] MOL2 format, chain U MOL2 format, chain V [auth U] mmCIF format, chain T [auth U] mmCIF format, chain U mmCIF format, chain V [auth U]	T [auth U], U, V [auth U]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain T [auth U] Focus chain U Focus chain V [auth U] Interactions & Density Focus chain T [auth U] Focus chain U Focus chain V [auth U]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-31

Deposition Author(s):

Barford, D.

Vazquez-Fernandez, E.

Zhang, Z.

Yang, J.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/6
Cancer Research UK	United Kingdom	C576/A14109

Revision History (Full details and data files)

Version 1.0: 2022-08-31
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Structure summary

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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.

8A3T | pdb_00008a3t

S. cerevisiae APC/C-Cdh1 complex

Literature

Cryo-EM structure of the S. cerevisiae APC/C-Cdh1 complex

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 14

UniProt

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Entity ID: 15

UniProt

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)