4H10 Transcription Dna date Sep 10, 2012
title Intermolecular Recognition Revealed By The Complex Structure Clock-Bmal1 Basic Helix-Loop-Helix Domains With E-Box Dna
authors Z.Wang, X.D.Su
compound source
Molecule: Aryl Hydrocarbon Receptor Nuclear Translocator-Li 1;
Chain: A
Fragment: Unp Residues 66-128
Synonym: Basic-Helix-Loop-Helix-Pas Protein Mop3, Brain And Arnt-Like 1, Class E Basic Helix-Loop-Helix Protein 5, Bhlh Of Pas Protein 3, Pas Domain-Containing Protein 3, Bhlh-Pas Jap3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Arntl, Bhlhe5, Bmal1, Mop3, Pasd3
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-21b

Molecule: Circadian Locomoter Output Cycles Protein Kaput
Chain: B
Fragment: Unp Residues 29-89
Synonym: Hclock, Class E Basic Helix-Loop-Helix Protein 8,
Ec: 2.3.1.48
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Clock, Bhlhe8, Kiaa0334
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-21b

Molecule: E-Box Dna Sense Strand
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Single-Strand Dna

Molecule: E-Box Dna Antisense Strand
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Single-Strand Dna
symmetry Space Group: P 31 2 1
R_factor 0.195 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.740 98.740 62.880 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand
enzyme Transferase E.C.2.3.1.48 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceIntermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA., Wang Z, Wu Y, Li L, Su XD, Cell Res. 2012 Dec 11. doi: 10.1038/cr.2012.170. PMID:23229515
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (4h10.pdb1.gz) 69 Kb
  • CSU: Contacts of Structural Units for 4H10
  • Structure Factors (100 Kb)
  • Retrieve 4H10 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4H10 from S2C, [Save to disk]
  • Re-refined 4h10 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4H10 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 4H10
  • 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 4H10, from MSDmotif at EBI
  • Fold representative 4h10 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4h10] [4h10_C] [4h10_B] [4h10_D] [4h10_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4H10: [HLH ] by SMART
  • Other resources with information on 4H10
  • Community annotation for 4H10 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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