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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6CIJ

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

Functional Information from GO Data
ChainGOidnamespacecontents
A0004519molecular_functionendonuclease activity
A0033151biological_processV(D)J recombination
A0043565molecular_functionsequence-specific DNA binding
A0046872molecular_functionmetal ion binding
A0061630molecular_functionubiquitin protein ligase activity
B0002313biological_processmature B cell differentiation involved in immune response
B0002326biological_processB cell lineage commitment
B0002331biological_processpre-B cell allelic exclusion
B0002358biological_processB cell homeostatic proliferation
B0002360biological_processT cell lineage commitment
B0003677molecular_functionDNA binding
B0003682molecular_functionchromatin binding
B0005515molecular_functionprotein binding
B0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
B0005547molecular_functionphosphatidylinositol-3,4,5-trisphosphate binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0006310biological_processDNA recombination
B0006325biological_processchromatin organization
B0008270molecular_functionzinc ion binding
B0030183biological_processB cell differentiation
B0030217biological_processT cell differentiation
B0033077biological_processT cell differentiation in thymus
B0033085biological_processnegative regulation of T cell differentiation in thymus
B0033151biological_processV(D)J recombination
B0035091molecular_functionphosphatidylinositol binding
B0042742biological_processdefense response to bacterium
B0043325molecular_functionphosphatidylinositol-3,4-bisphosphate binding
B0043565molecular_functionsequence-specific DNA binding
B0046622biological_processpositive regulation of organ growth
B0046872molecular_functionmetal ion binding
B0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
B0097519cellular_componentDNA recombinase complex
B0140002molecular_functionhistone H3K4me3 reader activity
C0004519molecular_functionendonuclease activity
C0033151biological_processV(D)J recombination
C0043565molecular_functionsequence-specific DNA binding
C0046872molecular_functionmetal ion binding
C0061630molecular_functionubiquitin protein ligase activity
D0002313biological_processmature B cell differentiation involved in immune response
D0002326biological_processB cell lineage commitment
D0002331biological_processpre-B cell allelic exclusion
D0002358biological_processB cell homeostatic proliferation
D0002360biological_processT cell lineage commitment
D0003677molecular_functionDNA binding
D0003682molecular_functionchromatin binding
D0005515molecular_functionprotein binding
D0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
D0005547molecular_functionphosphatidylinositol-3,4,5-trisphosphate binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0006310biological_processDNA recombination
D0006325biological_processchromatin organization
D0008270molecular_functionzinc ion binding
D0030183biological_processB cell differentiation
D0030217biological_processT cell differentiation
D0033077biological_processT cell differentiation in thymus
D0033085biological_processnegative regulation of T cell differentiation in thymus
D0033151biological_processV(D)J recombination
D0035091molecular_functionphosphatidylinositol binding
D0042742biological_processdefense response to bacterium
D0043325molecular_functionphosphatidylinositol-3,4-bisphosphate binding
D0043565molecular_functionsequence-specific DNA binding
D0046622biological_processpositive regulation of organ growth
D0046872molecular_functionmetal ion binding
D0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
D0097519cellular_componentDNA recombinase complex
D0140002molecular_functionhistone H3K4me3 reader activity
N0003677molecular_functionDNA binding
N0005634cellular_componentnucleus
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue ZN A 1101
ChainResidue
ACYS727
ACYS730
AHIS937
AHIS942
site_idAC2
Number of Residues3
Detailsbinding site for residue CA A 1102
ChainResidue
AASP600
AGLY601
FDT31
site_idAC3
Number of Residues4
Detailsbinding site for residue ZN C 1101
ChainResidue
CHIS937
CHIS942
CCYS727
CCYS730
site_idAC4
Number of Residues4
Detailsbinding site for residue CA C 1102
ChainResidue
CASP600
CGLY601
GDG41
GDT42
Functional Information from PROSITE/UniProt
site_idPS00353
Number of Residues12
DetailsHMG_BOX_1 HMG box A DNA-binding domain signature. FSKKCsERWKTM
ChainResidueDetails
NPHE41-MET52
site_idPS00435
Number of Residues11
DetailsPEROXIDASE_1 Peroxidases proximal heme-ligand signature. DTVYILGGHSL
ChainResidueDetails
DASP214-LEU224
site_idPS00518
Number of Residues10
DetailsZF_RING_1 Zinc finger RING-type signature. CkHlFCriCI
ChainResidueDetails
ACYS305-ILE314
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsSite: {"description":"Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues19
DetailsRegion: {"description":"Cytokine-stimulating activity","evidences":[{"source":"PubMed","id":"12765338","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues16
DetailsMotif: {"description":"Nuclear localization signal (NLS) 1","evidences":[{"source":"UniProtKB","id":"P63159","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsSite: {"description":"Cleavage; by thrombin:thrombomodulin","evidences":[{"source":"UniProtKB","id":"P10103","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsSite: {"description":"Cleavage; by CASP1","evidences":[{"source":"PubMed","id":"24474694","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues5
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P10103","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Cysteine sulfonic acid (-SO3H); alternate","evidences":[{"source":"UniProtKB","id":"P63159","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues3
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P63158","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues1
DetailsModified residue: {"description":"Cysteine sulfonic acid (-SO3H)","evidences":[{"source":"UniProtKB","id":"P63159","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues5
DetailsCross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-?)","evidences":[{"source":"PubMed","id":"29618516","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

246704

PDB entries from 2025-12-24

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