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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

1ID3

CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

Functional Information from GO Data
ChainGOidnamespacecontents
A0000500cellular_componentRNA polymerase I upstream activating factor complex
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005694cellular_componentchromosome
A0006325biological_processchromatin organization
A0006355biological_processregulation of DNA-templated transcription
A0006878biological_processintracellular copper ion homeostasis
A0008823molecular_functioncupric reductase (NADH) activity
A0009060biological_processaerobic respiration
A0009303biological_processrRNA transcription
A0030527molecular_functionstructural constituent of chromatin
A0042790biological_processnucleolar large rRNA transcription by RNA polymerase I
A0043505cellular_componentCENP-A containing nucleosome
A0043935biological_processsexual sporulation resulting in formation of a cellular spore
A0045943biological_processpositive regulation of transcription by RNA polymerase I
A0046982molecular_functionprotein heterodimerization activity
A0070911biological_processglobal genome nucleotide-excision repair
B0000500cellular_componentRNA polymerase I upstream activating factor complex
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005694cellular_componentchromosome
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0006355biological_processregulation of DNA-templated transcription
B0030527molecular_functionstructural constituent of chromatin
B0042790biological_processnucleolar large rRNA transcription by RNA polymerase I
B0042802molecular_functionidentical protein binding
B0045943biological_processpositive regulation of transcription by RNA polymerase I
B0046982molecular_functionprotein heterodimerization activity
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0000786cellular_componentnucleosome
C0003677molecular_functionDNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005694cellular_componentchromosome
C0006281biological_processDNA repair
C0006325biological_processchromatin organization
C0006974biological_processDNA damage response
C0030527molecular_functionstructural constituent of chromatin
C0031507biological_processheterochromatin formation
C0046982molecular_functionprotein heterodimerization activity
D0000786cellular_componentnucleosome
D0003677molecular_functionDNA binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005694cellular_componentchromosome
D0006325biological_processchromatin organization
D0006355biological_processregulation of DNA-templated transcription
D0030527molecular_functionstructural constituent of chromatin
D0046982molecular_functionprotein heterodimerization activity
E0000500cellular_componentRNA polymerase I upstream activating factor complex
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005694cellular_componentchromosome
E0006325biological_processchromatin organization
E0006355biological_processregulation of DNA-templated transcription
E0006878biological_processintracellular copper ion homeostasis
E0008823molecular_functioncupric reductase (NADH) activity
E0009060biological_processaerobic respiration
E0009303biological_processrRNA transcription
E0030527molecular_functionstructural constituent of chromatin
E0042790biological_processnucleolar large rRNA transcription by RNA polymerase I
E0043505cellular_componentCENP-A containing nucleosome
E0043935biological_processsexual sporulation resulting in formation of a cellular spore
E0045943biological_processpositive regulation of transcription by RNA polymerase I
E0046982molecular_functionprotein heterodimerization activity
E0070911biological_processglobal genome nucleotide-excision repair
F0000500cellular_componentRNA polymerase I upstream activating factor complex
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005694cellular_componentchromosome
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0006355biological_processregulation of DNA-templated transcription
F0030527molecular_functionstructural constituent of chromatin
F0042790biological_processnucleolar large rRNA transcription by RNA polymerase I
F0042802molecular_functionidentical protein binding
F0045943biological_processpositive regulation of transcription by RNA polymerase I
F0046982molecular_functionprotein heterodimerization activity
G0000122biological_processnegative regulation of transcription by RNA polymerase II
G0000786cellular_componentnucleosome
G0003677molecular_functionDNA binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005694cellular_componentchromosome
G0006281biological_processDNA repair
G0006325biological_processchromatin organization
G0006974biological_processDNA damage response
G0030527molecular_functionstructural constituent of chromatin
G0031507biological_processheterochromatin formation
G0046982molecular_functionprotein heterodimerization activity
H0000786cellular_componentnucleosome
H0003677molecular_functionDNA binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005694cellular_componentchromosome
H0006325biological_processchromatin organization
H0006355biological_processregulation of DNA-templated transcription
H0030527molecular_functionstructural constituent of chromatin
H0046982molecular_functionprotein heterodimerization activity
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN H 131
ChainResidue
GGLY45
GSER46
GGLY47
HSER93
HALA94
site_idAC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN C 132
ChainResidue
CARG89
site_idAC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN J 103
ChainResidue
JDG267
site_idAC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 147
ChainResidue
IDA133
IDG134
site_idAC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN I 148
ChainResidue
IDG70
site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN G 132
ChainResidue
GASP91
GGLU93
site_idAC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE MN I 149
ChainResidue
IDG121
site_idAC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 108
ChainResidue
JDA279
JDG280
site_idAC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN E 136
ChainResidue
EARG49
IDT8
site_idBC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN C 133
ChainResidue
CASP91
CGLU93
site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 111
ChainResidue
JDG216
JDG217
site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN I 150
ChainResidue
IDG78
JDG214
site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 113
ChainResidue
CASP73
JDC168
site_idBC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 114
ChainResidue
IDT45
JDG246
site_idBC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MN J 115
ChainResidue
JDT184
JDG185
JDG186
site_idBC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN D 131
ChainResidue
DGLU108
DHIS112
GGLU65
HHIS52
site_idBC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MN J 117
ChainResidue
JDA202
JDA203
Functional Information from PROSITE/UniProt
site_idPS00014
Number of Residues4
DetailsER_TARGET Endoplasmic reticulum targeting sequence. SQEL
ChainResidueDetails
CSER128-LEU131
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLtFPV
ChainResidueDetails
CALA22-VAL28
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
ALYS14-LEU20
site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlILpGELaKHAVSEG
ChainResidueDetails
DARG95-GLY117
site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues9
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues2
DetailsModified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"16768447","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"N6-glutaryllysine","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues2
DetailsSite: {"description":"Not ubiquitinated","evidences":[{"source":"PubMed","id":"10642555","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2201907","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues2
DetailsModified residue: {"description":"N5-methylglutamine","evidences":[{"source":"PubMed","id":"24352239","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsModified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"12535538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12535539","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14660635","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15280549","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

243911

PDB entries from 2025-10-29

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