6WCW Metal Binding Protein date Mar 31, 2020
title Structure Of Human Rubicon Rh Domain In Complex With Gtp-Bou
authors H.K.Bhargava, J.M.Byck, D.P.Farrell, I.Anishchenko, F.Dimaio, Y.J J.H.Hurley
compound source
Molecule: Ras-Related Protein Rab-7a
Chain: B
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab7a, Rab7
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693

Molecule: Run Domain Beclin-1-Interacting And Cysteine-Rich Containing Protein;
Chain: A
Fragment: Rh Domain
Synonym: Rubicon, Beclin-1 Associated Run Domain Containing Baron;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rubcn, Kiaa0226
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
symmetry Space Group: I 1 2 1
R_factor 0.200 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
60.040 45.330 186.277 90.00 98.51 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand GTP, MG, ZN enzyme
Primary referenceStructural basis for autophagy inhibition by the human Rubicon-Rab7 complex., Bhargava HK, Tabata K, Byck JM, Hamasaki M, Farrell DP, Anishchenko I, DiMaio F, Im YJ, Yoshimori T, Hurley JH, Proc Natl Acad Sci U S A. 2020 Jul 6. pii: 2008030117. doi:, 10.1073/pnas.2008030117. PMID:32632011
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (6wcw.pdb1.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 6WCW
  • CSU: Contacts of Structural Units for 6WCW
  • Structure Factors (360 Kb)
  • Retrieve 6WCW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6WCW from S2C, [Save to disk]
  • View 6WCW 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 6WCW
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6wcw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6wcw_A] [6wcw_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6WCW
  • Community annotation for 6WCW at PDBWiki (http://pdbwiki.org)

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