6R1U Gene Regulation date Mar 15, 2019
title Structure Of Lsd2npac-Linkernucleosome Core Particle Compl
authors C.Marabelli, S.Pilotto, S.Chittori, S.Subramaniam, A.Mattevi
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: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss

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: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss

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: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss

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: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Lysine-Specific Histone Demethylase 1b
Chain: K
Synonym: Flavin-Containing Amine Oxidase Domain-Containing Lysine-Specific Histone Demethylase 2;
Ec: 1.-.-.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm1b, Aof1, C6orf193, Lsd2
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss

Molecule: Putative Oxidoreductase Glyr1
Chain: L
Synonym: 3-Hydroxyisobutyrate Dehydrogenase-Like Protein,Cy Like Nuclear Factor N-Pac,Glyoxylate Reductase 1 Homolog,Nu Protein Np60,Nuclear Protein Of 60 Kda;
Ec: 1.-.-.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Glyr1, Hibdl, Np60
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Histone H3
Chain: M
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Xelaev_18002543mg
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plyss
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 4.36 Å
ligand FAD, ZN enzyme Oxidoreductase E.C.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E, M


C, G


F, B


H, D


K


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] (349 Kb) [Save to disk]
  • Biological Unit Coordinates (6r1u.pdb1.gz) 339 Kb
  • LPC: Ligand-Protein Contacts for 6R1U
  • CSU: Contacts of Structural Units for 6R1U
  • Retrieve 6R1U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6R1U from S2C, [Save to disk]
    • View 6R1U 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 6R1U
  • 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: [6r1u_H] [6r1u_D] [6r1u_G] [6r1u_F] [6r1u_A] [6r1u_J] [6r1u_I] [6r1u_C] [6r1u_B] [6r1u_K] [6r1u_M] [6r1u_E] [6r1u_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6R1U
  • Community annotation for 6R1U at PDBWiki (http://pdbwiki.org)

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