1GT0 Transcription date Jan 09, 2002
title Crystal Structure Of A Pouhmgdna Ternary Complex
authors A.Remenyi, M.Wilmanns
compound source
Molecule: 5'-D(Tptpcptptptpgptptptp Gpgpap Tpgpcptpapaptpgpgpgpa)-3';
Chain: A
Other_details: Fgf-4 Enhancer
Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: 5'-D(Aptpcpcpcpaptptpapgp Cpaptpcpcpapapapcpapapapgpa)-3';
Chain: B
Other_details: Fgf-4 Enhancer

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090

Molecule: Octamer-Binding Transcription Factor 1
Chain: C
Fragment: Pou Domain Residues 280-438
Synonym: Otf-1, Nf-A1, Oct-1
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet-24d

Molecule: Transcription Factor Sox-2
Chain: D
Fragment: Hmg Domain Residues 41-120
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet24-D
symmetry Space Group: P 31 2 1
R_factor 0.232 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.800 72.800 172.400 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.6 Å
note 1GT0 (Molecule of the Month:pdb112)
related structures by homologous chain: 1E3O, 1HF0, 1HRY
Primary referenceCrystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers., Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR, Wilmanns M, Genes Dev 2003 Aug 15;17(16):2048-59. PMID:12923055
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (1gt0.pdb1.gz) 57 Kb
  • CSU: Contacts of Structural Units for 1GT0
  • Likely Quarternary Molecular Structure file(s) for 1GT0
  • Structure Factors (116 Kb)
  • Retrieve 1GT0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GT0 from S2C, [Save to disk]
  • Re-refined 1gt0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GT0 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 1GT0
  • 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 1GT0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gt0c2, region C:3-77 [Jmol] [rasmolscript] [script source]
        - Domain d1gt0c1, region C:97-159 [Jmol] [rasmolscript] [script source]
        - Domain d1gt0d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1gt0 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: [1gt0] [1gt0_A] [1gt0_B] [1gt0_C] [1gt0_D]
  • SWISS-PROT database: [P14859] [P48432]
  • Domain organization of [PO2F1_HUMAN] [SOX2_MOUSE] by SWISSPFAM
  • Domains found in 1GT0: [HMG] [HOX] [POU ] by SMART
  • Alignments of the sequence of 1GT0 with the sequences similar proteins can be viewed for 1GT0's classification [PO2F1_HUMAN] [SOX2_MOUSE] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PO2F1_HUMAN] [SOX2_MOUSE] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1GT0
  • Community annotation for 1GT0 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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