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 0.230 R_Free 0.256
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 Diffraction	resolution	3.40 Å
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	ESCRT-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] (140 Kb) [Save to disk] Biological Unit Coordinates (2ymb.pdb1.gz) 68 Kb Biological Unit Coordinates (2ymb.pdb2.gz) 68 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

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 3D motif for 2YMB, from MSDmotif at EBI

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, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---