3EDV | pdb_00003edv

Crystal Structure of Repeats 14-16 of Beta2-Spectrin

PDB DOI: https://doi.org/10.2210/pdb3EDV/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-03 Released: 2009-01-20
Deposition Author(s): Michaely, P., Tomchick, D.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.250 (Depositor), 0.301 (DCC)
R-Value Work:
0.192 (Depositor), 0.257 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Localization and Structure of the Ankyrin-binding Site on beta2-Spectrin

Davis, L., Abdi, K., Machius, M., Brautigam, C., Tomchick, D.R., Bennett, V., Michaely, P.

(2009) J Biological Chem 284: 6982-6987

PubMed: 19098307 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M809245200
Primary Citation Related Structures:
3EDV

PubMed Abstract:
Spectrins are tetrameric actin-cross-linking proteins that form an elastic network, termed the membrane skeleton, on the cytoplasmic surface of cellular membranes. At the plasma membrane, the membrane skeleton provides essential support, preventing loss of membrane material to environmental shear stresses. The skeleton also controls the location, abundance, and activity of membrane proteins that are critical to cell and tissue function. The ability of the skeleton to modulate membrane stability and function requires adaptor proteins that bind the skeleton to membranes. The principal adaptors are the ankyrin proteins, which bind to the beta-subunit of spectrin and to the cytoplasmic domains of numerous integral membrane proteins. Here, we present the crystal structure of the ankyrin-binding domain of human beta2-spectrin at 1.95 A resolution together with mutagenesis data identifying the binding surface for ankyrins on beta2-spectrin.

Organizational Affiliation

Department of Cell Biology and Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA.

Macromolecule Content

Total Structure Weight: 76.28 kDa
Atom Count: 6,186
Modeled Residue Count: 643
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spectrin beta chain, brain 1	A, B	323	Homo sapiens	Mutation(s): 0 Gene Names: SPTBN1, SPTB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q01082 (Homo sapiens) Explore Q01082 Go to UniProtKB: Q01082
PHAROS: Q01082 GTEx: ENSG00000115306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01082
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] 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 B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] 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 B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] 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 B] mmCIF format, chain O [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [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 B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] 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 B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] 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 B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.250 (Depositor), 0.301 (DCC)
R-Value Work: 0.192 (Depositor), 0.257 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.335	α = 90
b = 56.415	β = 90
c = 261.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Michaely, P.

Tomchick, D.R.

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations