4TXR Protein Transport date Jul 04, 2014
title Crystal Structure Of Lip5 N-Terminal Domain Complexed With C And Chmp5 Mim
authors C.J.Vild, Z.Xu
compound source
Molecule: Charged Multivesicular Body Protein 1b
Chain: B
Fragment: Unp Residues 176-199
Synonym: Chmp1.5,Chromatin-Modifying Protein 1b,Chmp1b,Vacu Protein Sorting-Associated Protein 46-2,Hvps46-2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Chmp1b, C18orf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3

Molecule: Vacuolar Protein Sorting-Associated Protein Vta1
Chain: A
Fragment: Unp Residues 1-162
Synonym: Dopamine-Responsive Gene 1 Protein,Drg-1,Lyst-Inte Protein 5,Lip5,Skd1-Binding Protein 1,Sbp1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vta1, C6orf55, Hspc228, My012
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3

Molecule: Charged Multivesicular Body Protein 5
Chain: C
Fragment: Unp Residues 139-195
Synonym: Chromatin-Modifying Protein 5,Snf7 Domain-Containi 2,Vacuolar Protein Sorting-Associated Protein 60,Hvps60;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Chmp5, C9orf83, Snf7dc2, Cgi-34, Hspc177, Pnas-114, P
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3
symmetry Space Group: P 1 21 1
R_factor 0.164 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.197 60.567 52.048 90.00 90.39 90.00
method X-Ray Diffractionresolution 1.00 Å
ligand ACT, EDO enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceA Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5., Vild CJ, Li Y, Guo EZ, Liu Y, Xu Z, J Biol Chem. 2015 Jan 30. pii: jbc.M114.616730. PMID:25637630
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (4txr.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 4TXR
  • CSU: Contacts of Structural Units for 4TXR
  • Structure Factors (774 Kb)
  • Retrieve 4TXR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4TXR from S2C, [Save to disk]
  • Re-refined 4txr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4TXR 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 4TXR
  • 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 4TXR, from MSDmotif at EBI
  • Fold representative 4txr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4txr] [4txr_A] [4txr_C] [4txr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4TXR
  • Community annotation for 4TXR at PDBWiki (http://pdbwiki.org)

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