2NVU Protein Turnover, Ligase date Nov 13, 2006
title Structure Of Appbp1-Uba3~Nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex
authors D.T.Huang, H.W.Hunt, M.Zhuang, M.D.Ohi, J.M.Holton, B.A.Schulman
compound source
Molecule: Nedd8-Activating Enzyme E1 Regulatory Subunit
Chain: A
Synonym: Amyloid Protein-Binding Protein 1, Amyloid Beta Precursor Protein-Binding Protein 1, 59 Kda, App-Bp1, Protooncogene Protein 1, Hpp1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Appbp1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_vector: Bicistronic Pgex4t-3 Derivative
Expression_system_plasmid: Pgex4t-1

Molecule: Maltose Binding Proteinnedd8-Activating Enzyme E1 Catalytic Subunit Chimera;
Chain: B
Fragment: Residues 33-463
Synonym: Mbp, Ubiquitin-Activating Enzyme 3, Nedd8- Activating Enzyme E1c, Ubiquitin-Activating Enzyme E1c;
Ec: 6.3.2.-
Engineered: Yes
Other_details: Fusion Protein. Maltose Binding Protein (Residues 1001-1371), And The Nedd8-Activating Enzyme E1 Catalytic Subunit (Residues 2012-2442) Is From A Human Source;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube1c, Uba3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_vector: Bicistronic Pgex4t-3 Derivative
Expression_system_plasmid: Pgex4t-1

Molecule: Nedd8-Conjugating Enzyme Ubc12
Chain: C
Synonym: Ubiquitin-Conjugating Enzyme E2 M, Nedd8 Protein Ligase, Nedd8 Carrier Protein;
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2m, Ubc12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_vector: Bicistronic Pgex4t-3 Derivative
Expression_system_plasmid: Pgex4t-1

Molecule: Nedd8
Chain: I, J
Synonym: Ubiquitin-Like Protein Nedd8, Neddylin
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_vector: Bicistronic Pgex4t-3 Derivative
Expression_system_plasmid: Pgex4t-1
symmetry Space Group: P 32 2 1
R_factor 0.241 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
156.494 156.494 190.485 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand ATP, MG, ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


J, I


Primary referenceBasis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity., Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA, Nature. 2007 Jan 25;445(7126):394-8. Epub 2007 Jan 14. PMID:17220875
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (271 Kb) [Save to disk]
  • Biological Unit Coordinates (2nvu.pdb1.gz) 264 Kb
  • LPC: Ligand-Protein Contacts for 2NVU
  • CSU: Contacts of Structural Units for 2NVU
  • Likely Quarternary Molecular Structure file(s) for 2NVU
  • Structure Factors (550 Kb)
  • Retrieve 2NVU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NVU from S2C, [Save to disk]
  • Re-refined 2nvu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NVU 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 2NVU
  • 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 2NVU, from MSDmotif at EBI
  • Fold representative 2nvu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nvu_A] [2nvu_I] [2nvu_C] [2nvu_J] [2nvu_B] [2nvu]
  • SWISS-PROT database: [P0AEX9] [Q15843] [Q8TBC4] [P61081] [Q13564]
  • Belongs to the atp-binding cassette (abc) superfamily according to TCDB.
  • Domain organization of [MALE_ECOLI] [NEDD8_HUMAN] [UBA3_HUMAN] [UBC12_HUMAN] [ULA1_HUMAN] by SWISSPFAM
  • Domains found in 2NVU: [E2_bind] [UBCc] [UBQ ] by SMART
  • Other resources with information on 2NVU
  • Community annotation for 2NVU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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