5Z3U Structural Protein Hydrolase Dna date Jan 08, 2018
title Structure Of Snf2-Nucleosome Complex At Shl2 In Adp Befx Sta
authors M.Li, X.Xia, X.Liu, X.Li, Z.Chen
compound source
Molecule: Transcription Regulatory Protein Snf2
Chain: O
Synonym: Atp-Dependent Helicase Snf2,Regulatory Protein Gam Regulatory Protein Swi2,Swisnf Complex Component Snf2,Tran Factor Tye3;
Ec: 3.6.4.-
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Snf2, Gam1, Ric1, Swi2, Tye3, Yor290c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

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

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

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

Molecule: Dna (167-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (167-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.31 Å
ligand ADP, BEF, MG enzyme Hydrolase E.C.3.6.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


O


Primary referenceMechanism of DNA translocation underlying chromatin remodelling by Snf2., Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z, Nature. 2019 Mar;567(7748):409-413. doi: 10.1038/s41586-019-1029-2. Epub 2019 Mar, 13. PMID:30867599
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (342 Kb) [Save to disk]
  • Biological Unit Coordinates (5z3u.pdb1.gz) 335 Kb
  • LPC: Ligand-Protein Contacts for 5Z3U
  • CSU: Contacts of Structural Units for 5Z3U
  • Retrieve 5Z3U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Z3U from S2C, [Save to disk]
  • View 5Z3U 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 5Z3U
  • 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
  • Fold representative 5z3u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5z3u_O] [5z3u_H] [5z3u_D] [5z3u_C] [5z3u_B] [5z3u_J] [5z3u_A] [5z3u_G] [5z3u_F] [5z3u_E] [5z3u_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Z3U
  • Community annotation for 5Z3U at PDBWiki (http://pdbwiki.org)

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