3T7U | pdb_00003t7u

A NeW Crystal structure of APC-ARM

• PDB DOI: https://doi.org/10.2210/pdb3T7U/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-31 Released: 2011-12-14 
• Deposition Author(s): Zhang, Z., Wu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.313 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the armadillo repeat domain of adenomatous polyposis coli which reveals its inherent flexibility

Zhang, Z., Lin, K., Gao, L., Chen, L., Shi, X., Wu, G.

(2011) Biochem Biophys Res Commun 412: 732-736

• PubMed: 21871439 
• DOI: https://doi.org/10.1016/j.bbrc.2011.08.044
• Primary Citation Related Structures: 
  3T7U


• PubMed Abstract: 
  

  The conserved armadillo repeat (ARM) domain of adenomatous polyposis coli (APC) protein plays an important role in the recognition of its binding partners. In this study, we report the crystal structure of APC-ARM (residues 407-775), which was determined to 2.9 Å resolution. Our structure shows that the seven armadillo repeats of APC-ARM fold together into a compact domain, with Arm2 and Arm5 presenting some deviations from canonical armadillo repeats. There is a positively charged groove on the surface of APC-ARM, which might be the recognition site for APC-binding partners. Comparison of this structure with our previously reported structure of APC (407-751), together with normal mode analysis, reveals that the APC-ARM domain possesses a limited intrinsic flexibility. We propose that this intrinsic flexibility might be an inherent property of ARM domains in general.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.29 kDa 
• Atom Count: 4,807 
• Modeled Residue Count: 620 
• Deposited Residue Count: 756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	A, B	378	Homo sapiens	Mutation(s): 0  Gene Names: APC, DP2.5
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
PHAROS:  P25054 GTEx:  ENSG00000134982

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.313 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.496	α = 90
b = 72.496	β = 90
c = 129.981	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Zhang, Z., Wu, G.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Structure summary
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description