4NQA Transcription Regulator Dna date Nov 24, 2013
title Crystal Structure Of Liganded Hrxr-Alphahlxr-Beta Heterodim
authors X.H.Lou, G.Toresson, C.Benod, J.H.Suh, K.J.Phillips, P.Webb, J.A.G
compound source
Molecule: Retinoic Acid Receptor Rxr-Alpha
Chain: A, H
Fragment: Unp Residues 98-462
Synonym: Nuclear Receptor Subfamily 2 Group B Member 1, Ret Receptor Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rxra, Nr2b1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdf

Molecule: Liver X Nuclear Receptor Beta
Chain: B, I
Fragment: Unp Residues 72-461
Synonym: Nuclear Receptor Subfamily 1, Group H, Member 2, I Cra_c;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1h2, Hcg_22944
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet27

Molecule: Nuclear Receptor Coactivator 2
Chain: C, D, J, K
Fragment: Peptide (Unp Residues 686-698)
Synonym: Ncoa-2, Class E Basic Helix-Loop-Helix Protein 75, Transcriptional Intermediary Factor 2, Htif2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ncoa2, Bhlhe75, Tif2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: 5'-D(Tpapapgpgptpcpapcptptpcpapgpg -3';
Chain: E, L
Engineered: Yes
Other_details: Dr4 Dna Response Element

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpaptpgpapcpcptpgpapapgptpgpa -3';
Chain: F, M
Engineered: Yes
Other_details: Dr4 Dna Response Element

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43
R_factor 0.180 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.783 85.783 238.577 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand 965, 9CR, ZN enzyme
Gene HCG
Gene
Ontology
ChainFunctionProcessComponent
H, A


I, B


Primary referenceStructure of the retinoid X receptor alpha-liver X receptor beta (RXRalpha-LXRbeta) heterodimer on DNA., Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb P, Gustafsson JA, Nat Struct Mol Biol. 2014 Mar;21(3):277-81. doi: 10.1038/nsmb.2778. Epub 2014 Feb, 23. PMID:24561505
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (245 Kb) [Save to disk]
  • Biological Unit Coordinates (4nqa.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (4nqa.pdb2.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 4NQA
  • CSU: Contacts of Structural Units for 4NQA
  • Structure Factors (506 Kb)
  • Retrieve 4NQA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NQA from S2C, [Save to disk]
  • Re-refined 4nqa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NQA 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 4NQA
  • 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
  • 3D motif for 4NQA, from MSDmotif at EBI
  • Fold representative 4nqa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nqa_B] [4nqa_D] [4nqa_A] [4nqa] [4nqa_F] [4nqa_H] [4nqa_C] [4nqa_K] [4nqa_E] [4nqa_I] [4nqa_J] [4nqa_M] [4nqa_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NQA: [HOLI] [ZnF_C4 ] by SMART
  • Other resources with information on 4NQA
  • Community annotation for 4NQA at PDBWiki (http://pdbwiki.org)

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