3HYM | pdb_00003hym

Insights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure

PDB DOI: https://doi.org/10.2210/pdb3HYM/pdb

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

Deposited: 2009-06-22 Released: 2009-08-11
Deposition Author(s): Wang, J., Dye, B.T., Rajashankar, K.R., Kurinov, I., Schulman, B.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.220 (Depositor), 0.221 (DCC)
R-Value Work:
0.188 (Depositor), 0.194 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Insights into anaphase promoting complex TPR subdomain assembly from a CDC26-APC6 structure.

Wang, J., Dye, B.T., Rajashankar, K.R., Kurinov, I., Schulman, B.A.

(2009) Nat Struct Mol Biol 16: 987-989

PubMed: 19668213 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1645
Primary Citation Related Structures:
3HYM

PubMed Abstract:
The multisubunit anaphase promoting complex (APC) is an essential cell-cycle regulator. Although CDC26 is known to have a role in APC assembly, its molecular function has remained unclear. Biophysical, structural and genetic studies presented here reveal that CDC26 stabilizes the structure of APC6, a core TPR protein required for APC integrity. Notably, CDC26-APC6 association involves an intermolecular TPR mimic composed of one helix from each protein.

Organizational Affiliation

Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

Macromolecule Content

Total Structure Weight: 249.12 kDa
Atom Count: 15,517
Modeled Residue Count: 1,954
Deposited Residue Count: 2,154
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit CDC26	A, C, E, G, I A, C, E, G, I, K	29	Homo sapiens	Mutation(s): 0 Gene Names: CDC26, C9orf17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHZ8 (Homo sapiens) Explore Q8NHZ8 Go to UniProtKB: Q8NHZ8
PHAROS: Q8NHZ8 GTEx: ENSG00000176386
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NHZ8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein 16 homolog	B, D, F, H, J B, D, F, H, J, L	330	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 GTEx: ENSG00000130177
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13042
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, C, E, G, I A, C, E, G, I, K	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.220 (Depositor), 0.221 (DCC)
R-Value Work: 0.188 (Depositor), 0.194 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 301.897	α = 90
b = 301.897	β = 90
c = 80.168	γ = 120

Software Package:

Software Name	Purpose
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary