3GUT Transcription Dna date Mar 30, 2009
title Crystal Structure Of A Higher-Order Complex Of P50:Rela Boun Hiv-1 Ltr
authors J.C.Stroud, A.J.Oltman, A.Han, D.L.Bates, L.Chen
compound source
Molecule: Transcription Factor P65
Chain: A, C, E, G
Fragment: Unp Residues 20-291
Synonym: Nuclear Factor Nf-Kappa-B P65 Subunit
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nuclear Factor Nf-Kappa-B P105 Subunit
Chain: B, D, F, H
Fragment: Unp Residues 41-352
Synonym: Dna-Binding Factor Kbf1, Ebp-1, Nuclear Factor Nf- P50 Subunit;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hiv-Ltr Core Forward Strand
Chain: X, I
Other_details: Hiv-Ltr Core Forward Strand

Organism_scientific: Human Immunodeficiency Virus
Organism_common: Virus
Organism_taxid: 12721

Molecule: Hiv-Ltr Core Reverse Strand
Chain: Y, J
Other_details: Hiv-Ltr Core Reverse Strand

Organism_scientific: Human Immunodeficiency Virus
Organism_common: Virus
Organism_taxid: 12721
symmetry Space Group: P 42
R_factor 0.245 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
167.493 167.493 172.757 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.59 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceStructural Basis of HIV-1 Activation by NF-kappaB-A Higher-Order Complex of p50:RelA Bound to the HIV-1 LTR., Stroud JC, Oltman A, Han A, Bates DL, Chen L, J Mol Biol. 2009 Aug 14. PMID:19683540
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (423 Kb) [Save to disk]
  • Biological Unit Coordinates (3gut.pdb1.gz) 211 Kb
  • Biological Unit Coordinates (3gut.pdb2.gz) 211 Kb
  • CSU: Contacts of Structural Units for 3GUT
  • Structure Factors (720 Kb)
  • Retrieve 3GUT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GUT from S2C, [Save to disk]
  • Re-refined 3gut structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GUT 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 3GUT
  • 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 3GUT, from MSDmotif at EBI
  • Fold representative 3gut from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gut_D] [3gut_B] [3gut_C] [3gut_J] [3gut_I] [3gut] [3gut_H] [3gut_A] [3gut_G] [3gut_X] [3gut_F] [3gut_E] [3gut_Y]
  • SWISS-PROT database: [P19838] [Q04206]
  • Domain organization of [NFKB1_HUMAN] [TF65_HUMAN] by SWISSPFAM
  • Domain found in 3GUT: [IPT ] by SMART
  • Other resources with information on 3GUT
  • Community annotation for 3GUT 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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