3DBR	Cell Cycle	date	Jun 02, 2008
title	Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8'S E1 (Appbp1- Uba3arg190gln-Nedd8ala72arg)
authors	J.Souphron, B.A.Schulman
compound		source
Molecule: Nedd8-Activating Enzyme E1 Regulatory Subunit Chain: A, C, E, G Synonym: Amyloid Protein-Binding Protein 1, Amyloid Beta Protein-Binding Protein 1, 59 Kda, App-Bp1, Proto-Oncogene Protein 1; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nae1, Appbp1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Gold (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pablo
Molecule: Nedd8-Activating Enzyme E1 Catalytic Subunit Chain: B, D, F, H Fragment: Unp Residues 33-463 Synonym: Ubiquitin- Like Modifier-Activating Enzyme 3, Ubiquitin-Activating Enzyme 3, Nedd8-Activating Enzyme E1c, Ubiquitin-Activating Enzyme E1c; Ec: 6.3.2.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Uba3, Ube1c Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Gold (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pablo
Molecule: Nedd8 Chain: I, J, K, L Synonym: Ubiquitin-Like Protein Nedd8, Neddylin Engineered: Yes Mutation: 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 (Ril) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex2tk
symmetry	Space Group: P 21 21 21	R_factor 0.230 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 134.322 198.531 208.795 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.05 Å
ligand	ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A, E, C, G catalytic activity protein binding NEDD8 activating enzyme acti... ubiquitin protein ligase bin... protein heterodimerization a... DNA replication apoptotic process cell cycle signal transduction mitotic DNA replication chec... regulation of apoptotic proc... protein neddylation cytoplasm plasma membrane membrane F, B, H, D nucleotide binding catalytic activity protein binding ATP binding small protein activating enz... ligase activity acid-amino acid ligase activ... ligand-dependent nuclear rec... NEDD8 activating enzyme acti... protein heterodimerization a... mitotic cell cycle cellular protein modificatio... proteolysis cell cycle endomitotic cell cycle protein neddylation negative regulation of trans... regulation of cell cycle nucleus J, K, I, L ubiquitin protein ligase bin... regulation of transcription ... cellular protein modificatio... proteolysis ubiquitin-dependent protein ... protein localization anatomical structure morphog... response to organic cyclic c... protein neddylation nucleus
Primary reference	Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1., Souphron J, Waddell MB, Paydar A, Tokgoz-Gromley Z, Roussel MF, Schulman BA, Biochemistry. 2008 Jul 25. PMID:18652489

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (663 Kb) [Save to disk] Biological Unit Coordinates (3dbr.pdb1.gz) 170 Kb Biological Unit Coordinates (3dbr.pdb2.gz) 167 Kb Biological Unit Coordinates (3dbr.pdb3.gz) 170 Kb Biological Unit Coordinates (3dbr.pdb4.gz) 171 Kb LPC: Ligand-Protein Contacts for 3DBR CSU: Contacts of Structural Units for 3DBR Likely Quarternary Molecular Structure file(s) for 3DBR Structure Factors (1026 Kb) Retrieve 3DBR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DBR from S2C, [Save to disk] Re-refined 3dbr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DBR 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3DBR

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 3DBR, from MSDmotif at EBI Fold representative 3dbr from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dbr_A] [3dbr_B] [3dbr_C] [3dbr_D] [3dbr_E] [3dbr_F] [3dbr_G] [3dbr_H] [3dbr_I] [3dbr_J] [3dbr_K] [3dbr_L] SWISS-PROT database: [Q15843] [Q8TBC4] [Q13564] Domain organization of [NEDD8_HUMAN] [UBA3_HUMAN] [ULA1_HUMAN] by SWISSPFAM Domains found in 3DBR: [E2_bind] [UBQ ] by SMART Alignments of the sequence of 3DBR with the sequences similar proteins can be viewed for 3DBR's classification [NEDD8_HUMAN] [UBA3_HUMAN] [ULA1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [NEDD8_HUMAN] [UBA3_HUMAN] [ULA1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3DBR

Community annotation for 3DBR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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