Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

6DBI

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates

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
A0071702biological_processobsolete organic substance transport
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
C0071702biological_processobsolete organic substance transport
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 C 1101
ChainResidue
CCYS749
CCYS752
CHIS959
CHIS964

site_idAC2
Number of Residues5
Detailsbinding site for residue CA C 1102
ChainResidue
CGLU684
CASP730
CCA1103
GDT46
JDA16

site_idAC3
Number of Residues5
Detailsbinding site for residue CA C 1103
ChainResidue
CASP620
CGLY621
CCA1102
GDG45
GDT46

site_idAC4
Number of Residues4
Detailsbinding site for residue ZN A 1101
ChainResidue
ACYS749
ACYS752
AHIS959
AHIS964

site_idAC5
Number of Residues3
Detailsbinding site for residue CA A 1102
ChainResidue
AGLU684
ACA1103
IDA16

site_idAC6
Number of Residues5
Detailsbinding site for residue CA A 1103
ChainResidue
AASP620
AASP730
ACA1102
FDT35
IDA16

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

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

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

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

site_idSWS_FT_FI3
Number of Residues134
DetailsDNA_BIND: NBD => ECO:0000255|PROSITE-ProRule:PRU00820
ChainResidueDetails
CGLY408-GLN475
AGLY408-GLN475

site_idSWS_FT_FI4
Number of Residues28
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
CCYS272
CCYS331
CCYS334
CASP620
CASP730
CGLU984
ACYS272
AHIS276
ACYS296
ACYS299
AHIS301
CHIS276
ACYS311
AHIS313
ACYS316
ACYS319
ACYS331
ACYS334
AASP620
AASP730
AGLU984
CCYS296
CCYS299
CHIS301
CCYS311
CHIS313
CCYS316
CCYS319

site_idSWS_FT_FI5
Number of Residues8
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01101
ChainResidueDetails
CCYS361
CCYS366
CHIS378
CHIS382
ACYS361
ACYS366
AHIS378
AHIS382

site_idSWS_FT_FI6
Number of Residues2
DetailsSITE: Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site => ECO:0000250
ChainResidueDetails
CTRP915
ATRP915

222036

PDB entries from 2024-07-03

PDB statisticsPDBj update infoContact PDBjnumon