3UD1 | pdb_00003ud1

Crystal structure of ZU5A-ZU5B domains of human erythrocyte ankyrin

PDB DOI: https://doi.org/10.2210/pdb3UD1/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.206 (Depositor), 0.219 (DCC)
R-Value Work:
0.171 (Depositor), 0.187 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

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

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

(2012) J Mol Biology 417: 336-350

PubMed: 22310050 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2012.01.041
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 108.81 kDa
Atom Count: 8,547
Modeled Residue Count: 966
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin-1	A, B, C	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 GTEx: ENSG00000029534
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16157
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206 (Depositor), 0.219 (DCC)
R-Value Work: 0.171 (Depositor), 0.187 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.123	α = 90
b = 40.491	β = 112.68
c = 178.104	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Yasunaga, M.

Ipsaro, J.J.

Mondragon, A.

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2012-03-28
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description