6R25	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: 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: 562
Molecule: Npac Chain: L Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_taxid: 9606
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: 562
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: 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, Xelaev_18003602mg Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: H2b Chain: D, H Engineered: Yes		Organism_scientific: Xenopus Laevis Organism_common: African Clawed Frog Organism_taxid: 8355 Expression_system: Escherichia Coli Expression_system_taxid: 562
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
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 Microscopy	resolution	4.61 Å
ligand	FAD, ZN	enzyme	Oxidoreductase E.C.1 BRENDA
Gene Ontology	Chain Function Process Component A, E, M C, G F, B H, D K
Primary reference	A 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] (353 Kb) [Save to disk] Biological Unit Coordinates (6r25.pdb1.gz) 345 Kb LPC: Ligand-Protein Contacts for 6R25 CSU: Contacts of Structural Units for 6R25 Retrieve 6R25 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 6R25 from S2C, [Save to disk]

View 6R25 in 3D

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Visual 3D analysis of 6R25

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: [6r25_A] [6r25_B] [6r25_J] [6r25_D] [6r25_F] [6r25_L] [6r25_K] [6r25_I] [6r25_M] [6r25_H] [6r25_G] [6r25_E] [6r25_C] SWISS-PROT database: Domain organization of by SWISSPFAM

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