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6DBV

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs

Functional Information from GO Data
ChainGOidnamespacecontents
A0004519molecular_functionendonuclease activity
A0005515molecular_functionprotein binding
A0006974biological_processDNA damage response
A0008643biological_processcarbohydrate transport
A0015144molecular_functioncarbohydrate transmembrane transporter activity
A0015768biological_processmaltose transport
A0016020cellular_componentmembrane
A0030288cellular_componentouter membrane-bounded periplasmic space
A0033151biological_processV(D)J recombination
A0034219biological_processcarbohydrate transmembrane transport
A0034289biological_processdetection of maltose stimulus
A0042597cellular_componentperiplasmic space
A0042956biological_processmaltodextrin transmembrane transport
A0043190cellular_componentATP-binding cassette (ABC) transporter complex
A0043565molecular_functionsequence-specific DNA binding
A0046872molecular_functionmetal ion binding
A0055052cellular_componentATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
A0055085biological_processtransmembrane transport
A0060326biological_processcell chemotaxis
A0061630molecular_functionubiquitin protein ligase activity
A1901982molecular_functionmaltose binding
A1990060cellular_componentmaltose transport complex
B0003677molecular_functionDNA binding
B0003682molecular_functionchromatin binding
B0005515molecular_functionprotein binding
B0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
B0005547molecular_functionphosphatidylinositol-3,4,5-trisphosphate binding
B0005634cellular_componentnucleus
B0006310biological_processDNA recombination
B0006325biological_processchromatin organization
B0008270molecular_functionzinc ion binding
B0030098biological_processlymphocyte differentiation
B0030183biological_processB cell differentiation
B0030217biological_processT cell differentiation
B0033077biological_processT cell differentiation in thymus
B0033151biological_processV(D)J recombination
B0033152biological_processimmunoglobulin V(D)J recombination
B0035064molecular_functionmethylated histone binding
B0035091molecular_functionphosphatidylinositol binding
B0043325molecular_functionphosphatidylinositol-3,4-bisphosphate binding
B0043565molecular_functionsequence-specific DNA binding
B0046872molecular_functionmetal ion binding
B0048534biological_processhematopoietic or lymphoid organ development
B0048538biological_processthymus development
B0065004biological_processprotein-DNA complex assembly
B0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
B0097519cellular_componentDNA recombinase complex
B1905347cellular_componentendodeoxyribonuclease complex
B1990238molecular_functiondouble-stranded DNA endonuclease activity
C0004519molecular_functionendonuclease activity
C0005515molecular_functionprotein binding
C0006974biological_processDNA damage response
C0008643biological_processcarbohydrate transport
C0015144molecular_functioncarbohydrate transmembrane transporter activity
C0015768biological_processmaltose transport
C0016020cellular_componentmembrane
C0030288cellular_componentouter membrane-bounded periplasmic space
C0033151biological_processV(D)J recombination
C0034219biological_processcarbohydrate transmembrane transport
C0034289biological_processdetection of maltose stimulus
C0042597cellular_componentperiplasmic space
C0042956biological_processmaltodextrin transmembrane transport
C0043190cellular_componentATP-binding cassette (ABC) transporter complex
C0043565molecular_functionsequence-specific DNA binding
C0046872molecular_functionmetal ion binding
C0055052cellular_componentATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
C0055085biological_processtransmembrane transport
C0060326biological_processcell chemotaxis
C0061630molecular_functionubiquitin protein ligase activity
C1901982molecular_functionmaltose binding
C1990060cellular_componentmaltose transport complex
D0003677molecular_functionDNA binding
D0003682molecular_functionchromatin binding
D0005515molecular_functionprotein binding
D0005546molecular_functionphosphatidylinositol-4,5-bisphosphate binding
D0005547molecular_functionphosphatidylinositol-3,4,5-trisphosphate binding
D0005634cellular_componentnucleus
D0006310biological_processDNA recombination
D0006325biological_processchromatin organization
D0008270molecular_functionzinc ion binding
D0030098biological_processlymphocyte differentiation
D0030183biological_processB cell differentiation
D0030217biological_processT cell differentiation
D0033077biological_processT cell differentiation in thymus
D0033151biological_processV(D)J recombination
D0033152biological_processimmunoglobulin V(D)J recombination
D0035064molecular_functionmethylated histone binding
D0035091molecular_functionphosphatidylinositol binding
D0043325molecular_functionphosphatidylinositol-3,4-bisphosphate binding
D0043565molecular_functionsequence-specific DNA binding
D0046872molecular_functionmetal ion binding
D0048534biological_processhematopoietic or lymphoid organ development
D0048538biological_processthymus development
D0065004biological_processprotein-DNA complex assembly
D0080025molecular_functionphosphatidylinositol-3,5-bisphosphate binding
D0097519cellular_componentDNA recombinase complex
D1905347cellular_componentendodeoxyribonuclease complex
D1990238molecular_functiondouble-stranded DNA endonuclease activity
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue ZN A 1101
ChainResidue
ACYS749
ACYS752
AHIS959
AHIS964

site_idAC2
Number of Residues5
Detailsbinding site for residue CA A 1102
ChainResidue
AASP620
AHIS817
AGLU984
ACA1103
EDC17

site_idAC3
Number of Residues3
Detailsbinding site for residue CA A 1103
ChainResidue
AGLU984
ACA1102
EDC17

site_idAC4
Number of Residues5
Detailsbinding site for residue ZN C 1101
ChainResidue
CCYS752
CHIS766
CSER767
CILE768
CHIS964

site_idAC5
Number of Residues4
Detailsbinding site for residue CA C 1102
ChainResidue
CASP620
CGLY621
CGLU984
CCA1103

site_idAC6
Number of Residues3
Detailsbinding site for residue CA C 1103
ChainResidue
CASP620
CASP730
CCA1102

Functional Information from PROSITE/UniProt
site_idPS00518
Number of Residues10
DetailsZF_RING_1 Zinc finger RING-type signature. CrHlFCrlCI
ChainResidueDetails
CCYS311-ILE320
ACYS311-ILE320

site_idPS01037
Number of Residues18
DetailsSBP_BACTERIAL_1 Bacterial extracellular solute-binding proteins, family 1 signature. PIAvEalSLIYNkdlLpN
ChainResidueDetails
CPRO-9-ASN8
APRO-9-ASN8

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues138
DetailsZN_FING: PHD-type; atypical
ChainResidueDetails
BTRP416-LEU485
DTRP416-LEU485

site_idSWS_FT_FI2
Number of Residues16
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
BCYS419
DCYS423
DCYS446
DHIS453
DHIS456
DCYS459
DCYS479
DHIS482
BCYS423
BCYS446
BHIS453
BHIS456
BCYS459
BCYS479
BHIS482
DCYS419

site_idSWS_FT_FI3
Number of Residues67
DetailsDNA_BIND: NBD => ECO:0000255|PROSITE-ProRule:PRU00820
ChainResidueDetails
CGLY408-GLN475

site_idSWS_FT_FI4
Number of Residues14
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
CCYS272
CCYS331
CCYS334
CASP620
CASP730
CGLU984
CHIS276
CCYS296
CCYS299
CHIS301
CCYS311
CHIS313
CCYS316
CCYS319

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01101
ChainResidueDetails
CCYS361
CCYS366
CHIS378
CHIS382

site_idSWS_FT_FI6
Number of Residues1
DetailsSITE: Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site => ECO:0000250
ChainResidueDetails
CTRP915

224201

PDB entries from 2024-08-28

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