3C1C Structural Protein Dna date Jan 22, 2008
title The Effect Of H3 K79 Dimethylation And H4 K20 Trimethylation On Nucleosome And Chromatin Structure
authors X.Lu, M.Simon, J.Chodaparambil, J.Hansen, K.Shokat, K.Luger
compound source
Molecule: Histone H3-Like
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H3
Expression_system: Escherichia Coli

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H4
Expression_system: Escherichia Coli

Molecule: Histone H2a Type 1
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Histone H2a
Expression_system: Escherichia Coli

Molecule: Histone 2, H2bf
Chain: D, H
Engineered: Yes

Organism_scientific: Xenopus (Silurana) Tropicalis
Organism_common: Western Clawed Frog
Organism_taxid: 8364
Gene: Hist2h2bf, Tgas058p09.1-001
Expression_system: Escherichia Coli

Molecule: Palindromic 146bp Human Alpha Satellite Dna
Chain: I, J
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.030 110.080 182.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand M2L enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceThe effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure., Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K, Nat Struct Mol Biol. 2008 Oct;15(10):1122-4. Epub 2008 Sep 14. PMID:18794842
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (3c1c.pdb1.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 3C1C
  • CSU: Contacts of Structural Units for 3C1C
  • Likely Quarternary Molecular Structure file(s) for 3C1C
  • Structure Factors (544 Kb)
  • Retrieve 3C1C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C1C from S2C, [Save to disk]
  • Re-refined 3c1c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C1C 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 3C1C
  • 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 3C1C, from MSDmotif at EBI
  • Fold representative 3c1c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c1c] [3c1c_F] [3c1c_B] [3c1c_H] [3c1c_G] [3c1c_C] [3c1c_J] [3c1c_E] [3c1c_D] [3c1c_A] [3c1c_I]
  • SWISS-PROT database: [P06897] [P02302] [P62799] [Q28D68]
  • Domain organization of [H2A1_XENLA] [H3L_XENLA] [H4_XENLA] [Q28D68_XENTR] by SWISSPFAM
  • Domains found in 3C1C: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3C1C
  • Community annotation for 3C1C 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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