2NVU	Protein Turnover, Ligase	date	Nov 13, 2006
title	Structure Of Appbp1-Uba3~Nedd8-Nedd8-Mgatp-Ubc12(C111a), A T 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 Pr Protein-Binding Protein 1, 59 Kda, App-Bp1, Protooncogene P 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 E Catalytic Subunit Chimera; Chain: B Fragment: Residues 33-463 Synonym: Mbp, Ubiquitin-Activating Enzyme 3, Nedd8-Activati E1c, Ubiquitin-Activating Enzyme E1c; Ec: 6.3.2.- Engineered: Yes Other_details: Fusion Protein. Maltose Binding Protein (Res 1001-1371), And The Nedd8-Activating Enzyme E1 Catalytic Su (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 L 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 Diffraction	resolution	2.80 Å
ligand	ATP, MG, ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A B C J, I
Primary reference	Basis 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] (266 Kb) [Save to disk] Biological Unit Coordinates (2nvu.pdb1.gz) 259 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

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 3D motif for 2NVU, from MSDmotif at EBI

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)

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