3UD2

Crystal structure of Selenomethionine ZU5A-ZU5B protein domains of human erythrocyte ankyrin

• PDB DOI:  https://doi.org/10.2210/pdb3UD2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-27 Released: 2012-02-22 
• Deposition Author(s): Yasunaga, M., Ipsaro, J.J., Mondragon, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin.

Yasunaga, M., Ipsaro, J.J., Mondragon, A.

(2012) J Mol Biol 417: 336-350

• PubMed: 22310050 
• DOI: https://doi.org/10.1016/j.jmb.2012.01.041
• Primary Citation of Related Structures:  
  3UD1, 3UD2


• PubMed Abstract: 
  

The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through the adaptor protein ankyrin, which directly bridges the interaction between β-spectrin and membrane proteins. Ankyrins have a modular structure that includes two tandem ZU5 domains. The first domain, ZU5A, is directly responsible for binding β-spectrin. Here, we present a structure of the tandem ZU5 repeats of human erythrocyte ankyrin. Structural and biophysical experiments show that the second ZU5 domain, ZU5B, does not participate in spectrin binding. ZU5B is structurally similar to the ZU5 domain found in the netrin receptor UNC5b supramodule, suggesting that it could interact with other domains in ankyrin. Comparison of several ZU5 domains demonstrates that the ZU5 domain represents a compact and versatile protein interaction module.

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Organizational Affiliation: 

Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.57 kDa 
• Atom Count: 7,736 
• Modelled Residue Count: 963 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin-1	A [auth C], B, C [auth A]	326	Homo sapiens	Mutation(s): 1  Gene Names: ANK1, ANK
UniProt & NIH Common Fund Data Resources
Find proteins for P16157 (Homo sapiens) Explore P16157  Go to UniProtKB:  P16157
PHAROS:  P16157

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	AA [auth A], BA [auth A], E [auth C], F [auth C], G [auth C], Y [auth B], Z [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CL	Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth C], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth C], B, C [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.259 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.48	α = 90
b = 40.873	β = 92.01
c = 95.249	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Yasunaga, M., Ipsaro, J.J., Mondragon, A.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 1.2: 2019-12-25
  Changes: Database references, Derived calculations