1O9K Apoptosis date Dec 16, 2002
title Crystal Structure Of The Retinoblastoma Tumour Suppressor Protein Bound To E2f Peptide
authors B.Xiao, J.Spencer, A.Clements, N.Ali-Khan, S.Mittnacht, C.Broceno M.Burghammer, A.Perrakis, R.Marmorstein, S.J.Gamblin
compound source
Molecule: Retinoblastoma-Associated Protein
Chain: A, C, E, G
Fragment: Domain A, Residues 372-589
Synonym: P105-Rb, Prb
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Retinoblastoma-Associated Protein
Chain: B, D, F, H
Fragment: Domain B, Residues 636-787
Synonym: P105-Rb, Prb
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Factor E2f1
Chain: P, Q, R, S
Fragment: Residues 409-426
Synonym: Pbr3, Prb-Binding Protein E2f-1, Retinoblastoma-As Protein 1

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.229 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.996 158.548 110.617 90.00 93.70 90.00
method X-Ray Diffractionresolution 2.60 Å
related structures by homologous chain: 1AD6, 1N4M
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceCrystal structure of the retinoblastoma tumor suppressor protein bound to E2F and the molecular basis of its regulation., Xiao B, Spencer J, Clements A, Ali-Khan N, Mittnacht S, Broceno C, Burghammer M, Perrakis A, Marmorstein R, Gamblin SJ, Proc Natl Acad Sci U S A 2003 Mar 4;100(5):2363-8. PMID:12598654
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (1o9k.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (1o9k.pdb2.gz) 62 Kb
  • Biological Unit Coordinates (1o9k.pdb3.gz) 62 Kb
  • Biological Unit Coordinates (1o9k.pdb4.gz) 62 Kb
  • CSU: Contacts of Structural Units for 1O9K
  • Likely Quarternary Molecular Structure file(s) for 1O9K
  • Structure Factors (393 Kb)
  • Retrieve 1O9K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O9K from S2C, [Save to disk]
  • Re-refined 1o9k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1O9K 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 1O9K
  • 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 1O9K, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o9ka_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1o9kb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1o9kc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1o9kd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1o9ke_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1o9kf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1o9kg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1o9kh_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1o9k 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: [1o9k_R] [1o9k_B] [1o9k_E] [1o9k_F] [1o9k_H] [1o9k_P] [1o9k_G] [1o9k] [1o9k_C] [1o9k_S] [1o9k_D] [1o9k_Q] [1o9k_A]
  • SWISS-PROT database: [Q01094] [P06400]
  • Domain organization of [E2F1_HUMAN] [RB_HUMAN] by SWISSPFAM
  • Domains found in 1O9K: [CYCLIN] [RB_A ] by SMART
  • Other resources with information on 1O9K
  • Community annotation for 1O9K 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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