General information
PDB ID 6R25
Title STRUCTURE OF LSD2/NPAC-LINKER/NUCLEOSOME CORE PARTICLE COMPLEX: CLASS 3
PDB header GENE REGULATION
Date 2019-03-15
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.61
Kind dna
Organism HOMO SAPIENS, XENOPUS LAEVIS, SYNTHETIC CONSTRUCT
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6r25.pdb KLMABCDEFGH IJ 0
Biounits:
6r25.pdb1.pdb KLMABCDEFGH IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P84233_37-132 4e-46 1 CL0012 A 37 131 IJ   
CENP-T_C Domain P62799_26-99 4.4e-08 1 CL0012 B 26 98 IJ   
Histone Domain P06897_19-91 1.5e-15 1 CL0012 C 17 90 J   
Histone Domain P02281_33-102 1.8e-22 1 CL0012 D 25 98 IJ   
Histone Domain P84233_37-132 1.8e-46 1 CL0012 E 36 131 IJ   
CENP-T_C Domain P62799_26-99 4.6e-08 1 CL0012 F 26 98 IJ   
Histone Domain P06897_5-91 3e-16 1 CL0012 G 8 90 IJ   
Histone Domain P02281_28-102 8.1e-23 1 CL0012 H 24 98 JI   
Amino_oxidase Domain Q8NB78_392-820 7.6e-89 1 CL0063 K 392 820   
zf-CW Domain Q8NB78_138-191 2.4e-10 1 No_clan K 138 191   
SWIRM Domain Q8NB78_281-364 9e-07 1 CL0123 K 281 364   
Histone_H2A_C Family P06897_92-120 7.7e-19 1 No_clan C 91 120   
Histone_H2A_C Family P06897_92-120 9e-19 1 No_clan G 91 120   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E/M=2-136 C nucleoplasm
A/E/M=2-136 C nucleosome
A/E/M=2-136 F DNA binding
A/E/M=2-136 F protein heterodimerization activity
B/F=2-103 C host cell nucleus
B/F=2-103 C nucleosome
B/F=2-103 C nucleus
B/F=2-103 F DNA binding
B/F=2-103 F protein heterodimerization activity
B/F=2-103 P DNA-templated transcription, initiation
C/G=2-130 C nucleosome
C/G=2-130 C nucleus
C/G=2-130 F DNA binding
C/G=2-130 F protein heterodimerization activity
D/H=1-126 C nucleosome
D/H=1-126 C nucleus
D/H=1-126 F DNA binding
D/H=1-126 F protein heterodimerization activity
K=51-822 C nuclear chromatin
K=51-822 C nucleoplasm
K=51-822 C nucleosome
K=51-822 C nucleus
K=51-822 F chromatin binding
K=51-822 F FAD binding
K=51-822 F flavin adenine dinucleotide binding
K=51-822 F histone binding
K=51-822 F histone demethylase activity (H3-dimethyl-K4 specific)
K=51-822 F histone demethylase activity (H3-monomethyl-K4 specific)
K=51-822 F oxidoreductase activity
K=51-822 F transcription factor binding
K=51-822 F zinc ion binding
K=51-822 P DNA methylation involved in gamete generation
K=51-822 P histone H3-K4 demethylation
K=51-822 P multicellular organism development
K=51-822 P negative regulation of transcription by RNA polymerase II
K=51-822 P positive regulation of transcription by RNA polymerase II
K=51-822 P protein deubiquitination
K=51-822 P regulation of DNA methylation
K=51-822 P regulation of gene expression by genetic imprinting
L=214-225 C cytosol
L=214-225 C nucleoplasm
L=214-225 C nucleosome
L=214-225 F chromatin binding
L=214-225 F DNA binding
L=214-225 F histone binding
L=214-225 F methylated histone binding
L=214-225 F NAD binding
L=214-225 F NADP binding
L=214-225 F nucleosome binding
L=214-225 F oxidoreductase activity
L=214-225 P positive regulation of histone acetylation
L=214-225 P positive regulation of transcription by RNA polymerase II
Sequences
Download file with secondary structure created by Stride  
6r25.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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