3A5M Contractile Protein date Aug 09, 2009
title Crystal Structure Of A Dictyostelium P109i Mg2+-Actin In Com Human Gelsolin Segment 1
authors K.Murakami, T.Yasunaga, T.Q.Noguchi, T.Q.Uyeda, T.Wakabayashi
compound source
Molecule: Gelsolin
Chain: S
Fragment: Gelsolin-Like 1, Residues 53-176
Synonym: Actin-Depolymerizing Factor, Adf, Brevin, Agel
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Peikl

Molecule: Major Actin
Chain: C
Synonym: Actin-1, Actin-2, Actin-2-Sub 1, Actin-4, Actin-5, Actin-7, Actin-8, Actin A8, Actin-Iel1, Actin-9, Actin-11, Actin A12, Actin-13, Actin-14, Actin-15, Actin A1, Actin II 3a, Actin-16, Actin M6, Actin-19, Actin-20, Actin-21;
Engineered: Yes
Mutation: Yes

Organism_scientific: Dictyostelium Discoideum
Organism_common: Slime Mold
Organism_taxid: 44689
Expression_system: Dictyostelium
Expression_system_taxid: 5782
Expression_system_vector_type: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.701 69.173 181.690 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ATP, CA, HIC, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceStructural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release., Murakami K, Yasunaga T, Noguchi TQ, Gomibuchi Y, Ngo KX, Uyeda TQ, Wakabayashi T, Cell. 2010 Oct 15;143(2):275-87. PMID:20946985
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3a5m.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 3A5M
  • CSU: Contacts of Structural Units for 3A5M
  • Structure Factors (206 Kb)
  • Retrieve 3A5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A5M from S2C, [Save to disk]
  • Re-refined 3a5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A5M 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.
  • Visual 3D analysis of 3A5M
  • 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 3A5M, from MSDmotif at EBI
  • Fold representative 3a5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a5m] [3a5m_S] [3a5m_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3A5M: [ACTIN] [GEL ] by SMART
  • Other resources with information on 3A5M
  • Community annotation for 3A5M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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