1Z5S Ligase date Mar 19, 2005
title Crystal Structure Of A Complex Between Ubc9, Sumo-1, Rangap1 And Nup358ranbp2
authors D.Reverter, C.D.Lima
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 I
Chain: A
Synonym: Ubiquitin-Protein Ligase I, Ubiquitin Carrier Protein I, Sumo-1-Protein Ligase, Sumo- 1 Conjugating Enzyme, Ubiquitin Carrier Protein 9, P18;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2i, Ubc9, Ubce9
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ubiquitin-Like Protein Smt3c
Chain: B
Synonym: Ubiquitin-Homology Domain Protein Pic1, Ubiquitin- Like Protein Ubl1, Ubiquitin-Related Protein Sumo-1, Gap Modifying Protein 1, Gmp1, Sentrin, Oksw-Cl.43;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubl1, Smt3c, Smt3h3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ran Gtpase-Activating Protein 1
Chain: C
Fragment: C-Terminal Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rangap1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3

Molecule: Ran-Binding Protein 2
Chain: D
Fragment: Ir1-M Domain
Synonym: Ranbp2, Nuclear Pore Complex Protein Nup358, Nucleoporin Nup358, 358 Kda Nucleoporin, P270;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ranbp2, Nup358
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3
symmetry Space Group: P 32 2 1
R_factor 0.247 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.123 157.123 59.613 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.01 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • SUMO conjugating enzyme acti...


  • C


    Primary referenceInsights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex., Reverter D, Lima CD, Nature 2005 Jun 2;435(7042):687-92. PMID:15931224
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (1z5s.pdb1.gz) 74 Kb
  • CSU: Contacts of Structural Units for 1Z5S
  • Likely Quarternary Molecular Structure file(s) for 1Z5S
  • Structure Factors (135 Kb)
  • Retrieve 1Z5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Z5S from S2C, [Save to disk]
  • Re-refined 1z5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Z5S 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 1Z5S
  • 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 1Z5S, from MSDmotif at EBI
  • Fold representative 1z5s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1z5s_B] [1z5s_D] [1z5s_A] [1z5s_C] [1z5s]
  • SWISS-PROT database: [P46060] [P49792] [P63165] [P63279]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Belongs to the peroxisomal protein importer (ppi) family according to TCDB.
  • Domain organization of [RAGP1_HUMAN] [RBP2_HUMAN] [SUMO1_HUMAN] [UBC9_HUMAN] by SWISSPFAM
  • Domains found in 1Z5S: [UBCc] [UBQ ] by SMART
  • Other resources with information on 1Z5S
  • Community annotation for 1Z5S at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • 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
    Bioinformatics Unit
    Weizmann Institute of Science