5SZI Endocytosis date Aug 14, 2016
title Structure Of Human Rab8a In Complex With The Bmerb Domain Of
authors A.Rai, A.Oprisko, J.Campos, Y.Fu, T.Friese, A.Itzen, R.S.Goody, M.P E.M.Gazdag
compound source
Molecule: Ras-Related Protein Rab-8a
Chain: A
Synonym: Oncogene C-Mel
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab8a, Mel, Rab8
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Mical C-Terminal-Like Protein
Chain: B
Synonym: Erk2-Binding Testicular Protein 1,Ebitein-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Micalcl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.237 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.400 122.400 139.150 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand GNP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referencebMERB domains are bivalent Rab8 family effectors evolved by gene duplication., Rai A, Oprisko A, Campos J, Fu Y, Friese T, Itzen A, Goody RS, Gazdag EM, Muller MP, Elife. 2016 Aug 23;5. pii: e18675. doi: 10.7554/eLife.18675. PMID:27552051
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (5szi.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 5SZI
  • CSU: Contacts of Structural Units for 5SZI
  • Structure Factors (111 Kb)
  • Retrieve 5SZI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5SZI from S2C, [Save to disk]
  • Re-refined 5szi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5SZI 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 5SZI
  • 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
  • Fold representative 5szi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5szi_A] [5szi] [5szi_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5SZI: [DUF3585] [RAB ] by SMART
  • Other resources with information on 5SZI
  • Community annotation for 5SZI at PDBWiki (http://pdbwiki.org)

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