6R1T Gene Regulation date Mar 15, 2019
title Structure Of Lsd2npac-Linkernucleosome Core Particle Compl 1, Free Nuclesome
authors C.Marabelli, S.Pilotto, S.Chittori, S.Subramaniam, A.Mattevi
compound source
Molecule: Histone H3
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Xelaev_18002543mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
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, Xelaev_18003602mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b
Chain: D, H
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Xelaev_18032686mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_common: African Clawed Frog
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_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 3.70 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceA Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex., Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A, Cell Rep. 2019 Apr 9;27(2):387-399.e7. doi: 10.1016/j.celrep.2019.03.061. PMID:30970244
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (6r1t.pdb1.gz) 215 Kb
  • CSU: Contacts of Structural Units for 6R1T
  • Retrieve 6R1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6R1T from S2C, [Save to disk]
  • View 6R1T 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 6R1T
  • 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 6r1t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6r1t_D] [6r1t_G] [6r1t_F] [6r1t_E] [6r1t_A] [6r1t_I] [6r1t_J] [6r1t_C] [6r1t_B] [6r1t_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6R1T
  • Community annotation for 6R1T at PDBWiki (http://pdbwiki.org)

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