1GA5 Transcription Dna date Nov 29, 2000
title Crystal Structure Of The Orphan Nuclear Receptor Rev-Erb(Alp Binding Domain Bound To Its Cognate Response Element
authors M.L.Sierk, Q.Zhao, F.Rastinejad
compound source
Molecule: 5'-D(Cpapapcptpapgpgptpcpapcptpapg Apg)-3';
Chain: C, G
Engineered: Yes
Synthetic: Yes
Other_details: Synthesized Optimal Dr2 Target

Molecule: 5'-D(Cptpgpapcpcptpapgptpgpapcpcpt (5it)Pg)-3';
Chain: D, H
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Optimal Dr2 Target Complementary With 5-Iodo-Thymidine;

Molecule: Orphan Nuclear Receptor Nr1d1
Chain: A, B, E, F
Fragment: Dna-Binding Domain Plus C-Terminal Extension
Synonym: Rev-Erb(Alpha)
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nr1d1 Or Thral Or Ear1 Or Hrev
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex
symmetry Space Group: P 1
R_factor 0.253 R_Free 0.299
length a length b length c angle alpha angle beta angle gamma
44.920 52.020 78.880 85.84 76.61 74.48
method X-Ray Diffractionresolution 2.40 Å
ligand 5IU, ZN enzyme
related structures by homologous chain: 1A6Y, 1HLZ
F, A, E, B

Primary referenceDNA deformability as a recognition feature in the reverb response element., Sierk ML, Zhao Q, Rastinejad F, Biochemistry 2001 Oct 30;40(43):12833-43. PMID:11669620
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (1ga5.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (1ga5.pdb2.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 1GA5
  • CSU: Contacts of Structural Units for 1GA5
  • Likely Quarternary Molecular Structure file(s) for 1GA5
  • Structure Factors (223 Kb)
  • Retrieve 1GA5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GA5 from S2C, [Save to disk]
  • Re-refined 1ga5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GA5 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 1GA5
  • 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 1GA5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ga5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ga5b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ga5e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ga5f_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1ga5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ga5_B] [1ga5_F] [1ga5_H] [1ga5_E] [1ga5_C] [1ga5_G] [1ga5_D] [1ga5] [1ga5_A]
  • SWISS-PROT database: [P20393]
  • Domain organization of [NR1D1_HUMAN] by SWISSPFAM
  • Domain found in 1GA5: [ZnF_C4 ] by SMART
  • Other resources with information on 1GA5
  • Community annotation for 1GA5 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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