5VPE Transcription Dna date May 04, 2017
title Transcription Factor Fosbjund Bzip Domain In Complex With C Dna, Type-I Crystal
authors Z.Yin, M.Machius, G.Rudenko
compound source
Molecule: Protein Fosb
Chain: C, A
Fragment: Unp Residues 153-219
Synonym: G0g1 Switch Regulatory Protein 3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fosb, G0s3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21-Nesg

Molecule: Transcription Factor Jun-D
Chain: D, B
Fragment: Unp Residues 266-332
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Jund
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a

Molecule: Dna (5'- D(Cpgptpcpgpgptpgpapcptpcpapcpcpgpapcpg)
Chain: G, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'- D(Cpgptpcpgpgptpgpapgptpcpapcpcpgpapcpg)
Chain: H, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.218 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.479 90.755 105.618 90.00 117.93 90.00
method X-Ray Diffractionresolution 2.05 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceActivator Protein-1: redox switch controlling structure and DNA-binding., Yin Z, Machius M, Nestler EJ, Rudenko G, Nucleic Acids Res. 2017 Sep 7. doi: 10.1093/nar/gkx795. PMID:28981703
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (236 Kb) [Save to disk]
  • Biological Unit Coordinates (5vpe.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (5vpe.pdb2.gz) 116 Kb
  • CSU: Contacts of Structural Units for 5VPE
  • Structure Factors (1560 Kb)
  • Retrieve 5VPE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VPE from S2C, [Save to disk]
  • View 5VPE 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 5VPE
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5vpe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vpe_F] [5vpe_A] [5vpe_G] [5vpe_B] [5vpe_D] [5vpe_E] [5vpe_C] [5vpe_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VPE
  • Community annotation for 5VPE at PDBWiki (http://pdbwiki.org)

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