OCA Atlas for 3ZWH

3ZWH

Ca-Binding Protein Motor Protein

date

Jul 31, 2011

title

Ca2+-Bound S100a4 C3s, C81s, C86s And F45w Mutant Complexed With Myosin Iia

authors

B.Kiss, A.Duelli, L.Radnai, A.K.Kekesi, G.Katona, L.Nyitray

compound

source

Molecule: Protein S100-A4
Chain: A, B
Synonym: Calvasculin, Metastasin, Placental Calcium-Binding Protein, Protein Mts1, S100 Calcium-Binding Protein A4, S1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbh4

Molecule: Myosin-9
Chain: Q
Fragment: Residues 1893-1935
Synonym: Cellular Myosin Heavy Chain\,Type A, Myosin Heavy Myosin Heavy Chain\,Non-Muscle Iia, Non-Muscle Myosin Heav A, Nmmhc-A, Non-Muscle Myosin Heavy Chain Iia, Nmmhc II-A, Nmmhc-Iia;
Engineered: Yes
Mutation: Yes

symmetry

Space Group: P 41 21 2

R_factor

0.1753

R_Free

0.2064

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
63.972	63.972	138.984	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.94 Å

ligand

ACT, AZI, CA

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, B	calcium ion binding protein binding identical protein binding metal ion binding calcium-dependent protein bi... RAGE receptor binding	epithelial to mesenchymal tr... positive regulation of I-kap...	nucleus neuron projection perinuclear region of cytopl...

Primary reference

Crystal structure of the S100A4-nonmuscle myosin IIA tail fragment complex reveals an asymmetric target binding mechanism., Kiss B, Duelli A, Radnai L, Kekesi KA, Katona G, Nyitray L, Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6048-53. Epub 2012 Mar 28. PMID:22460785

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]

Biological Unit Coordinates (3zwh.pdb1.gz) 83 Kb

LPC: Ligand-Protein Contacts for 3ZWH

CSU: Contacts of Structural Units for 3ZWH

Structure Factors (166 Kb)

Retrieve 3ZWH in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3ZWH from S2C, [Save to disk]

Re-refined 3zwh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ZWH in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3ZWH

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 3ZWH, from MSDmotif at EBI

Fold representative 3zwh from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3zwh_A] [3zwh_B] [3zwh_Q]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Alignments of the sequence of 3ZWH with the sequences similar proteins can be viewed for 3ZWH's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3ZWH

Community annotation for 3ZWH at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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