6FML Dna Binding Protein date Jan 31, 2018
title Cryoem Structure Ino80core Nucleosome Complex
authors S.Eustermann, K.Schall, D.Kostrewa, M.Strauss, K.Hopfner
compound source
Molecule: Ruvb-Like Helicase
Chain: A, B, C
Ec: 3.6.4.12
Engineered: Yes
 Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Gene: Ctht_0006820
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Ruvb-Like Helicase
Chain: D, E, F
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Gene: Ctht_0006170
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Ino80
Chain: G
Engineered: Yes
Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Les2
Chain: H
Engineered: Yes
Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719), Chaetomium Thermophilum Var. Thermoph 1495;
Organism_taxid: 759272
Gene: Ctht_0004910
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Ies6
Chain: I
Engineered: Yes
Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Gene: Ctht_0032670
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Actin Related Protein 5
Chain: J
Engineered: Yes
Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719), Chaetomium Thermophilum Var. Thermoph 1495;
Organism_taxid: 759272
Gene: Ctht_0032660
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Nucleosomal Dna Strand 1
Chain: K
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Nucleosomal Dna Strand 2
Chain: L
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Histone H3.2
Chain: M, Q
Synonym: Histone H3m,Histone H3o
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist2h3a, Hist2h3c, H3f2, H3fm, Hist2h3d
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: N, R
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1
Chain: O, S
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-Cefgi
Chain: P, T
Synonym: Histone H2b.1 A,Histone H2b.A,H2ba,Histone H2b.G, Histone H2b.H,H2bh,Histone H2b.K,H2bk,Histone H2b.L,H2bl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bc, H2bfl, Hist1h2be, H2bfh, Hist1h2bf, H2bfg, Hist1h2bg, H2bfa, Hist1h2bi, H2bfk;
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 4.34 Å
ligand ADP, ATP enzyme Hydrolase E.C.3.6.4.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
C, A, B
  • DNA helicase activity
  • 5'-3' DNA helicase activity


    • F, E, D
  • DNA helicase activity
  • 5'-3' DNA helicase activity


    • G


    H


    I


    N, R


    Q, M


    S, O


    T, P


    Primary referenceStructural basis for ATP-dependent chromatin remodelling by the INO80 complex., Eustermann S, Schall K, Kostrewa D, Lakomek K, Strauss M, Moldt M, Hopfner KP, Nature. 2018 Apr;556(7701):386-390. doi: 10.1038/s41586-018-0029-y. Epub 2018 Apr, 11. PMID:29643509
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (803 Kb) [Save to disk]
  • Biological Unit Coordinates (6fml.pdb1.gz) 784 Kb
  • LPC: Ligand-Protein Contacts for 6FML
  • CSU: Contacts of Structural Units for 6FML
  • Retrieve 6FML in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FML from S2C, [Save to disk]
    • View 6FML 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 6FML
  • 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: [6fml_M] [6fml_C] [6fml_B] [6fml_F] [6fml_H] [6fml_O] [6fml_S] [6fml_N] [6fml_K] [6fml_R] [6fml_E] [6fml_I] [6fml_G] [6fml_Q] [6fml_P] [6fml_A] [6fml_T] [6fml_J] [6fml_D] [6fml_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6FML
  • Community annotation for 6FML at PDBWiki (http://pdbwiki.org)

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