7QE7

High-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1

PDB DOI: https://doi.org/10.2210/pdb7QE7/pdb
EM Map EMD-13931: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2021-12-01 Released: 2022-01-26
Deposition Author(s): Hoefler, A., Yu, J., Chang, L., Zhang, Z., Yang, J., Boland, A., Barford, D.
Funding Organization(s): Swiss National Science Foundation, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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

High-resolution structure of the Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

Hoefler, A., Yu, J., Chang, L., Zhang, Z., Yang, J., Boland, A., Barford, D.

To be published.

Macromolecule Content

Total Structure Weight: 1,279.09 kDa
Atom Count: 71,432
Modelled Residue Count: 8,928
Deposited Residue Count: 11,302
Unique protein chains: 16

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 10	A [auth L]	185	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC10, APC10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM13 (Homo sapiens) Explore Q9UM13 Go to UniProtKB: Q9UM13
PHAROS: Q9UM13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UM13
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 15	B [auth D]	121	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC15, C11orf51, HSPC020
UniProt & NIH Common Fund Data Resources
Find proteins for P60006 (Homo sapiens) Explore P60006 Go to UniProtKB: P60006
PHAROS: P60006
Entity Groups
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UniProt Group	P60006
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 1	C [auth A]	1,944	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC1, TSG24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A4 (Homo sapiens) Explore Q9H1A4 Go to UniProtKB: Q9H1A4
PHAROS: Q9H1A4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1A4
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 2	D [auth N]	822	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC2, APC2, KIAA1406
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX6 (Homo sapiens) Explore Q9UJX6 Go to UniProtKB: Q9UJX6
PHAROS: Q9UJX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJX6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 4	E [auth I]	814	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC4, APC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX5 (Homo sapiens) Explore Q9UJX5 Go to UniProtKB: Q9UJX5
PHAROS: Q9UJX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJX5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 5	F [auth O]	755	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC5, APC5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX4 (Homo sapiens) Explore Q9UJX4 Go to UniProtKB: Q9UJX4
PHAROS: Q9UJX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJX4
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box only protein 5	G [auth S]	447	Homo sapiens	Mutation(s): 0 Gene Names: FBXO5, EMI1, FBX5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKT4 (Homo sapiens) Explore Q9UKT4 Go to UniProtKB: Q9UKT4
PHAROS: Q9UKT4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UKT4
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein 16 homolog	H [auth K], O [auth Q]	620	Homo sapiens	Mutation(s): 0 Gene Names: CDC16, ANAPC6
UniProt & NIH Common Fund Data Resources
Find proteins for Q13042 (Homo sapiens) Explore Q13042 Go to UniProtKB: Q13042
PHAROS: Q13042
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13042
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC26	I [auth G], J [auth W]	85	Homo sapiens	Mutation(s): 0 Gene Names: CDC26, ANAPC12, C9orf17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHZ8 (Homo sapiens) Explore Q8NHZ8 Go to UniProtKB: Q8NHZ8
PHAROS: Q8NHZ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NHZ8
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 13	K [auth M]	74	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BS18 (Homo sapiens) Explore Q9BS18 Go to UniProtKB: Q9BS18
PHAROS: Q9BS18
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BS18
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 16	L [auth H]	110	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC16, C10orf104, CENP-27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DE5 (Homo sapiens) Explore Q96DE5 Go to UniProtKB: Q96DE5
PHAROS: Q96DE5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96DE5
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein 27 homolog	M [auth J], N [auth P]	824	Homo sapiens	Mutation(s): 0 Gene Names: CDC27, ANAPC3, D0S1430E, D17S978E
UniProt & NIH Common Fund Data Resources
Find proteins for P30260 (Homo sapiens) Explore P30260 Go to UniProtKB: P30260
PHAROS: P30260
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30260
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 7	P [auth Y], S [auth Z]	599	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC7, APC7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX3 (Homo sapiens) Explore Q9UJX3 Go to UniProtKB: Q9UJX3
PHAROS: Q9UJX3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJX3
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein 23 homolog	Q [auth U], R [auth V]	597	Homo sapiens	Mutation(s): 0 Gene Names: CDC23, ANAPC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX2 (Homo sapiens) Explore Q9UJX2 Go to UniProtKB: Q9UJX2
PHAROS: Q9UJX2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJX2
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Fizzy-related protein homolog	T [auth R]	496	Homo sapiens	Mutation(s): 0 Gene Names: FZR1, CDH1, FYR, FZR, KIAA1242
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM11 (Homo sapiens) Explore Q9UM11 Go to UniProtKB: Q9UM11
PHAROS: Q9UM11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UM11
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 11	U [auth C]	84	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC11, HSPC214
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYG5 (Homo sapiens) Explore Q9NYG5 Go to UniProtKB: Q9NYG5
PHAROS: Q9NYG5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NYG5
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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 AA [auth C] SDF format, chain V [auth N] SDF format, chain W [auth S] SDF format, chain X [auth S] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain V [auth N] MOL2 format, chain W [auth S] MOL2 format, chain X [auth S] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] V [auth N] W [auth S] X [auth S] Y [auth C] AA [auth C], V [auth N], W [auth S], X [auth S], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain V [auth N] Focus chain W [auth S] Focus chain X [auth S] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain V [auth N] Focus chain W [auth S] Focus chain X [auth S] Focus chain Y [auth C] Focus chain Z [auth C]