4KUD Structural Protein Transcription Dna date May 22, 2013
title Crystal Structure Of N-Terminal Acetylated Sir3 Bah Domain D Mutant In Complex With Yeast Nucleosome Core Particle
authors D.Yang, Q.Fang, M.Wang, R.Ren, H.Wang, M.He, Y.Sun, N.Yang, R.M.Xu
compound source
Molecule: Histone H3
Chain: A, E
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Hht1, Ybr010w, Ybr0201, Hht2, Sin2, Ynl031c, N2749
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Hhf1, Ybr009c, Ybr0122, Hhf2, Ynl030w, N2752
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Histone H2a.2
Chain: C, G
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Hta2, H2a2, Ybl003c, Ybl0103
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Histone H2b.1
Chain: D, H
Synonym: Suppressor Of Ty Protein 12
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Htb1, H2b1, Spt12, Ydr224c, Yd9934.09c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Nucloesome Dna
Chain: I, J
Engineered: Yes

Synthetic: Yes

Molecule: Regulatory Protein Sir3
Chain: K, L
Fragment: Bah Domain, Unp Residues 2-219
Synonym: Silent Information Regulator 3
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Sir3, Cmt1, Mar2, Ste8, Ylr442c, L9753.10
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell: Sf21
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 61
R_factor 0.198 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.330 108.330 498.920 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
ligand AYA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K, L


Primary referenceNalpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain., Yang D, Fang Q, Wang M, Ren R, Wang H, He M, Sun Y, Yang N, Xu RM, Nat Struct Mol Biol. 2013 Aug 11. doi: 10.1038/nsmb.2637. PMID:23934152
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (323 Kb) [Save to disk]
  • Biological Unit Coordinates (4kud.pdb1.gz) 316 Kb
  • LPC: Ligand-Protein Contacts for 4KUD
  • CSU: Contacts of Structural Units for 4KUD
  • Structure Factors (1325 Kb)
  • Retrieve 4KUD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KUD from S2C, [Save to disk]
  • Re-refined 4kud structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KUD 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 4KUD
  • 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 4KUD, from MSDmotif at EBI
  • Fold representative 4kud from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kud_H] [4kud_D] [4kud_I] [4kud_A] [4kud_B] [4kud_F] [4kud_K] [4kud_L] [4kud_E] [4kud] [4kud_C] [4kud_J] [4kud_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KUD: [BAH] [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 4KUD
  • Community annotation for 4KUD at PDBWiki (http://pdbwiki.org)

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