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 Diffractionresolution 3.05 Å
ligand ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


J, K, I, L


Primary referenceStructural 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.
  • 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_F] [3dbr_A] [3dbr_E] [3dbr_I] [3dbr_B] [3dbr_K] [3dbr_J] [3dbr] [3dbr_H] [3dbr_G] [3dbr_L] [3dbr_D] [3dbr_C]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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