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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

1F66

2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005694cellular_componentchromosome
A0030527molecular_functionstructural constituent of chromatin
A0031492molecular_functionnucleosomal DNA binding
A0031507biological_processheterochromatin formation
A0046982molecular_functionprotein heterodimerization activity
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005694cellular_componentchromosome
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0030527molecular_functionstructural constituent of chromatin
B0032991cellular_componentprotein-containing complex
B0043505cellular_componentCENP-A containing nucleosome
B0046982molecular_functionprotein heterodimerization activity
B0061644biological_processprotein localization to CENP-A containing chromatin
C0000786cellular_componentnucleosome
C0000791cellular_componenteuchromatin
C0000792cellular_componentheterochromatin
C0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
C0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
C0001740cellular_componentBarr body
C0003677molecular_functionDNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005694cellular_componentchromosome
C0006325biological_processchromatin organization
C0030527molecular_functionstructural constituent of chromatin
C0031490molecular_functionchromatin DNA binding
C0031492molecular_functionnucleosomal DNA binding
C0031507biological_processheterochromatin formation
C0045944biological_processpositive regulation of transcription by RNA polymerase II
C0046982molecular_functionprotein heterodimerization activity
C0070062cellular_componentextracellular exosome
C0071392biological_processcellular response to estradiol stimulus
D0000786cellular_componentnucleosome
D0002227biological_processinnate immune response in mucosa
D0003677molecular_functionDNA binding
D0005515molecular_functionprotein binding
D0005615cellular_componentextracellular space
D0005634cellular_componentnucleus
D0005694cellular_componentchromosome
D0006325biological_processchromatin organization
D0019731biological_processantibacterial humoral response
D0030527molecular_functionstructural constituent of chromatin
D0031507biological_processheterochromatin formation
D0046982molecular_functionprotein heterodimerization activity
D0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005694cellular_componentchromosome
E0030527molecular_functionstructural constituent of chromatin
E0031492molecular_functionnucleosomal DNA binding
E0031507biological_processheterochromatin formation
E0046982molecular_functionprotein heterodimerization activity
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005694cellular_componentchromosome
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0030527molecular_functionstructural constituent of chromatin
F0032991cellular_componentprotein-containing complex
F0043505cellular_componentCENP-A containing nucleosome
F0046982molecular_functionprotein heterodimerization activity
F0061644biological_processprotein localization to CENP-A containing chromatin
G0000786cellular_componentnucleosome
G0000791cellular_componenteuchromatin
G0000792cellular_componentheterochromatin
G0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
G0000979molecular_functionRNA polymerase II core promoter sequence-specific DNA binding
G0001740cellular_componentBarr body
G0003677molecular_functionDNA binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005654cellular_componentnucleoplasm
G0005694cellular_componentchromosome
G0006325biological_processchromatin organization
G0030527molecular_functionstructural constituent of chromatin
G0031490molecular_functionchromatin DNA binding
G0031492molecular_functionnucleosomal DNA binding
G0031507biological_processheterochromatin formation
G0045944biological_processpositive regulation of transcription by RNA polymerase II
G0046982molecular_functionprotein heterodimerization activity
G0070062cellular_componentextracellular exosome
G0071392biological_processcellular response to estradiol stimulus
H0000786cellular_componentnucleosome
H0002227biological_processinnate immune response in mucosa
H0003677molecular_functionDNA binding
H0005515molecular_functionprotein binding
H0005615cellular_componentextracellular space
H0005634cellular_componentnucleus
H0005694cellular_componentchromosome
H0006325biological_processchromatin organization
H0019731biological_processantibacterial humoral response
H0030527molecular_functionstructural constituent of chromatin
H0031507biological_processheterochromatin formation
H0046982molecular_functionprotein heterodimerization activity
H0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN E 1001
ChainResidue
DVAL1245
EHOH240
EHOH241
EHOH242
EASP677
FHOH327
site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MN I 1002
ChainResidue
IDG39
IDG40
IHOH1022
site_idAC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 1003
ChainResidue
IDG70
IDG71
site_idAC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 1004
ChainResidue
IDA99
IDG100
site_idAC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 1005
ChainResidue
IDG121
IHOH1060
site_idAC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN I 1006
ChainResidue
IDG134
site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MN I 1007
ChainResidue
IDG137
IDG138
IHOH1027
site_idAC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 1008
ChainResidue
JDG185
JDG186
site_idAC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN J 1010
ChainResidue
JDG217
site_idBC1
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN J 1011
ChainResidue
JDG246
site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 1012
ChainResidue
JDG267
JDG268
site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 1013
ChainResidue
JDG280
JHOH1059
site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MN C 1014
ChainResidue
CHOH104
CHIS912
CHIS914
site_idBC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN G 1128
ChainResidue
GHIS1112
GHIS1114
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA823-VAL829
site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18
site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS414-LEU420
site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG1289-GLY1311
site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO466-ILE474
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsModified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsLipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues6
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"17947660","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18034455","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues2
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"18034455","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23806337","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues5
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62803","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues22
DetailsRegion: {"description":"M6 cassette"}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues20
DetailsRegion: {"description":"Required for interaction with INCENP","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues2
DetailsModified residue: {"description":"N6-lactoyllysine","evidences":[{"source":"PubMed","id":"31645732","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"11835281","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues2
DetailsGlycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

246031

PDB entries from 2025-12-10

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