3VVW Protein Transport date Jul 28, 2012
title Ndp52 In Complex With Lc3c
authors M.Akutsu, N.V.Muhlinen, F.Randow, D.Komander
compound source
Molecule: Calcium-Binding And Coiled-Coil Domain-Containing 2;
Chain: A
Fragment: Unp Residues 21-141
Synonym: Antigen Nuclear Dot 52 Kda Protein, Nuclear Domain Protein Ndp52, Nuclear Domain 10 Protein 52, Nuclear Dot Pr
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Calcoco2, Ndp52
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Microtubule-Associated Proteins 1a1b Light Chain
Chain: B
Fragment: Unp Residues 1-126
Synonym: Autophagy-Related Protein Lc3 C, Autophagy-Related Ubiquitin-Like Modifier Lc3 C, Map1 Light Chain 3-Like Prot Map1amap1b Light Chain 3 C, Map1amap1b Lc3 C, Microtubule Associated Protein 1 Light Chain 3 Gamma;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map1lc3c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.210 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
195.720 37.420 40.280 90.00 94.66 90.00
method X-Ray Diffractionresolution 2.50 Å

Primary referenceLC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy., von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein A, Bloor S, Rutherford TJ, Freund SM, Komander D, Randow F, Mol Cell. 2012 Nov 9;48(3):329-42. doi: 10.1016/j.molcel.2012.08.024. Epub 2012, Sep 27. PMID:23022382
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (3vvw.pdb1.gz) 76 Kb
  • CSU: Contacts of Structural Units for 3VVW
  • Structure Factors (540 Kb)
  • Retrieve 3VVW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VVW from S2C, [Save to disk]
  • Re-refined 3vvw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VVW 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 3VVW
  • 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 3VVW, from MSDmotif at EBI
  • Fold representative 3vvw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vvw] [3vvw_A] [3vvw_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VVW
  • Community annotation for 3VVW at PDBWiki (http://pdbwiki.org)

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