5V1Y Protein Binding date Mar 02, 2017
title Crystal Structure Of The Ternary Rpn13 Pru-Rpn2 (940-953)-Ub Complex
authors C.W.Hemmis, R.T.Vanderlinden, T.Yao, H.Robinson, C.P.Hill
compound source
Molecule: Proteasomal Ubiquitin Receptor Adrm1
Chain: A, B
Fragment: Pru Domain (Unp Residues 19-132)
Synonym: 110 Kda Cell Membrane Glycoprotein, Gp110, Adhesio Regulating Molecule 1, Arm-1, Proteasome Regulatory Particl Atpase 13, Hrpn13, Rpn13 Homolog;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adrm1, Gp110
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21 Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet151

Molecule: Ubiquitin
Chain: C, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21 Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: 26s Proteasome Non-Atpase Regulatory Subunit 1
Chain: E, F
Fragment: C-Termimal Domain (Unp Residues 940-953)
Synonym: 26s Proteasome Regulatory Subunit Rpn2, 26s Protea Regulatory Subunit S1, 26s Proteasome Subunit P112, Rpn2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Psmd1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21 Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet151
symmetry Space Group: P 1 21 1
R_factor 0.140 R_Free 0.175
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.129 96.098 57.605 90.00 96.38 90.00
method X-Ray Diffractionresolution 1.42 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism., VanderLinden RT, Hemmis CW, Yao T, Robinson H, Hill CP, J Biol Chem. 2017 Apr 25. pii: jbc.M117.785287. doi: 10.1074/jbc.M117.785287. PMID:28442575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (5v1y.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (5v1y.pdb2.gz) 103 Kb
  • CSU: Contacts of Structural Units for 5V1Y
  • Structure Factors (1830 Kb)
  • Retrieve 5V1Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V1Y from S2C, [Save to disk]
  • Re-refined 5v1y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5V1Y 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 5V1Y
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v1y_E] [5v1y_B] [5v1y_F] [5v1y_C] [5v1y] [5v1y_A] [5v1y_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V1Y
  • Community annotation for 5V1Y at PDBWiki (http://pdbwiki.org)

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