2YMB Protein Transport date Oct 08, 2012
title Structures Of Mitd1
authors M.A.Hadders, M.Agromayor, T.Obita, O.Perisic, A.Caballe, M.Kloc, M.H.Lamers, R.L.Williams, J.Martin-Serrano
compound source
Molecule: Mit Domain-Containing Protein 1
Chain: A, B, C, D
Synonym: Mitd1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: C41

Molecule: Charged Multivesicular Body Protein 1a
Chain: F, H
Fragment: Mim1, Residues 56-68
Synonym: Chmp1a, Chromatin-Modifying Protein 1a, Chmp1a, Va Protein Sorting-Associated Protein 46-1, Vps46-1, Hvps46-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: C41
symmetry Space Group: I 2 3
R_factor 0.2296 R_Free 0.2561
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.046 222.046 222.046 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceESCRT-III binding protein MITD1 is involved in cytokinesis and has an unanticipated PLD fold that binds membranes., Hadders MA, Agromayor M, Obita T, Perisic O, Caballe A, Kloc M, Lamers MH, Williams RL, Martin-Serrano J, Proc Natl Acad Sci U S A. 2012 Oct 8. PMID:23045692
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (2ymb.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (2ymb.pdb2.gz) 69 Kb
  • CSU: Contacts of Structural Units for 2YMB
  • Structure Factors (350 Kb)
  • Retrieve 2YMB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YMB from S2C, [Save to disk]
  • Re-refined 2ymb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YMB 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 2YMB
  • 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 2YMB, from MSDmotif at EBI
  • Fold representative 2ymb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ymb_F] [2ymb_H] [2ymb_C] [2ymb_A] [2ymb_B] [2ymb] [2ymb_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YMB: [MIT ] by SMART
  • Other resources with information on 2YMB
  • Community annotation for 2YMB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science