5E5A Protein Binding Viral Protein Dna date Oct 08, 2015
title Crystal Structure Of The Chromatin-Tethering Domain Of Human Cytomegalovirus Ie1 Protein Bound To The Nucleosome Core Pa
authors Q.Fang, P.Chen, M.Wang, J.Fang, N.Yang, G.Li, R.M.Xu
compound source
Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Humam
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5a

Molecule: Histone H3.2
Chain: A, E
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

Molecule: C-Terminal Domain Of Regulatory Protein Ie1
Chain: K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human Herpesvirus 5 Strain Towne
Organism_common: Hhv-5
Organism_taxid: 10363
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.700 109.474 181.976 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceHuman cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome., Fang Q, Chen P, Wang M, Fang J, Yang N, Li G, Xu RM, Elife. 2016 Jan 26;5. pii: e11911. doi: 10.7554/eLife.11911. PMID:26812545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (256 Kb) [Save to disk]
  • Biological Unit Coordinates (5e5a.pdb1.gz) 249 Kb
  • LPC: Ligand-Protein Contacts for 5E5A
  • CSU: Contacts of Structural Units for 5E5A
  • Structure Factors (2260 Kb)
  • Retrieve 5E5A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E5A from S2C, [Save to disk]
  • Re-refined 5e5a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5E5A 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 5E5A
  • 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
  • Fold representative 5e5a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e5a_H] [5e5a_G] [5e5a_C] [5e5a_F] [5e5a_A] [5e5a_K] [5e5a_I] [5e5a_B] [5e5a_E] [5e5a] [5e5a_D] [5e5a_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5E5A: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 5E5A
  • Community annotation for 5E5A at PDBWiki (http://pdbwiki.org)

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