4O6X | pdb_00004o6x

Crystal structure of human Ankyrin G death domain

• PDB DOI: https://doi.org/10.2210/pdb4O6X/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-24 Released: 2014-10-29 
• Deposition Author(s): Liu, Y., Zhang, Y., Wang, J.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Ankyrin G death domain.

Liu, Y., Zhang, Y., Wang, J.H.

(2014) Proteins 82: 3476-3482

• PubMed: 25307106 
• DOI: https://doi.org/10.1002/prot.24702
• Primary Citation Related Structures: 
  4O6X


• PubMed Abstract: 
  

  Ankyrins (Ank) are a ubiquitously expressed family of multifunctional membrane adapter proteins. Ankyrin G (AnkG) is critical for assembling and maintenance of the axon initial segment. Here we present the 2.1 Å crystal structure of human AnkG death domain (hAnkG-DD). The core death domain is composed of six α-helices and three 3₁₀-helices. It forms a hydrophobic pocket on the surface of the molecule. The C-terminal tail of the hAnkG-DD curves back to have the aromatic ring of a phenylalanine residue, Phe100 insert into this pocket, which anchors the flexible tail onto the core domain. Related DDs were selected for structure comparison. The major variations are at the C-terminal region, including the α6 and the long C-terminal extension. The results of size exclusion chromatography and analytical ultracentrifugation suggest that hAnkG-DD exists as monomer in solution. Our work should help for the future investigation of the structure-function of AnkG.

---

Organizational Affiliation: 
• State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.64 kDa 
• Atom Count: 1,606 
• Modeled Residue Count: 193 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin-3	A, B	121	Homo sapiens	Mutation(s): 0  Gene Names: ANK3, Ankyrin G
UniProt & NIH Common Fund Data Resources
Find proteins for Q12955 (Homo sapiens) Explore Q12955  Go to UniProtKB:  Q12955
PHAROS:  Q12955 GTEx:  ENSG00000151150

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.452	α = 90
b = 56.817	β = 90
c = 81.949	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Liu, Y., Zhang, Y., Wang, J.H.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Other
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description