5Z3O Structural Protein Hydrolase Dna date Jan 08, 2018
title Structure Of Snf2-Nucleosome Complex In Adp State
authors M.Li, X.Xia, X.Liu, X.Li, Z.Chen
compound source
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

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 (Strain Atcc S288c);
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
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 3.62 Å
ligand ADP, 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] (336 Kb) [Save to disk]
  • Biological Unit Coordinates (5z3o.pdb1.gz) 330 Kb
  • LPC: Ligand-Protein Contacts for 5Z3O
  • CSU: Contacts of Structural Units for 5Z3O
  • Retrieve 5Z3O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Z3O from S2C, [Save to disk]
    • View 5Z3O 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 5Z3O
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5z3o_O] [5z3o_D] [5z3o_I] [5z3o_G] [5z3o_B] [5z3o_C] [5z3o_J] [5z3o_F] [5z3o_A] [5z3o_E] [5z3o_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Z3O
  • Community annotation for 5Z3O at PDBWiki (http://pdbwiki.org)

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