6CIJ
Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004519 | molecular_function | endonuclease activity |
A | 0033151 | biological_process | V(D)J recombination |
A | 0043565 | molecular_function | sequence-specific DNA binding |
A | 0046872 | molecular_function | metal ion binding |
A | 0061630 | molecular_function | ubiquitin protein ligase activity |
B | 0002313 | biological_process | mature B cell differentiation involved in immune response |
B | 0002326 | biological_process | B cell lineage commitment |
B | 0002331 | biological_process | pre-B cell allelic exclusion |
B | 0002358 | biological_process | B cell homeostatic proliferation |
B | 0002360 | biological_process | T cell lineage commitment |
B | 0003677 | molecular_function | DNA binding |
B | 0003682 | molecular_function | chromatin binding |
B | 0005515 | molecular_function | protein binding |
B | 0005546 | molecular_function | phosphatidylinositol-4,5-bisphosphate binding |
B | 0005547 | molecular_function | phosphatidylinositol-3,4,5-trisphosphate binding |
B | 0005634 | cellular_component | nucleus |
B | 0005654 | cellular_component | nucleoplasm |
B | 0006310 | biological_process | DNA recombination |
B | 0006325 | biological_process | chromatin organization |
B | 0008270 | molecular_function | zinc ion binding |
B | 0030183 | biological_process | B cell differentiation |
B | 0030217 | biological_process | T cell differentiation |
B | 0033077 | biological_process | T cell differentiation in thymus |
B | 0033085 | biological_process | negative regulation of T cell differentiation in thymus |
B | 0033151 | biological_process | V(D)J recombination |
B | 0035064 | molecular_function | methylated histone binding |
B | 0035091 | molecular_function | phosphatidylinositol binding |
B | 0035265 | biological_process | organ growth |
B | 0042742 | biological_process | defense response to bacterium |
B | 0043325 | molecular_function | phosphatidylinositol-3,4-bisphosphate binding |
B | 0046622 | biological_process | positive regulation of organ growth |
B | 0046872 | molecular_function | metal ion binding |
B | 0080025 | molecular_function | phosphatidylinositol-3,5-bisphosphate binding |
B | 1904155 | biological_process | DN2 thymocyte differentiation |
C | 0004519 | molecular_function | endonuclease activity |
C | 0033151 | biological_process | V(D)J recombination |
C | 0043565 | molecular_function | sequence-specific DNA binding |
C | 0046872 | molecular_function | metal ion binding |
C | 0061630 | molecular_function | ubiquitin protein ligase activity |
D | 0002313 | biological_process | mature B cell differentiation involved in immune response |
D | 0002326 | biological_process | B cell lineage commitment |
D | 0002331 | biological_process | pre-B cell allelic exclusion |
D | 0002358 | biological_process | B cell homeostatic proliferation |
D | 0002360 | biological_process | T cell lineage commitment |
D | 0003677 | molecular_function | DNA binding |
D | 0003682 | molecular_function | chromatin binding |
D | 0005515 | molecular_function | protein binding |
D | 0005546 | molecular_function | phosphatidylinositol-4,5-bisphosphate binding |
D | 0005547 | molecular_function | phosphatidylinositol-3,4,5-trisphosphate binding |
D | 0005634 | cellular_component | nucleus |
D | 0005654 | cellular_component | nucleoplasm |
D | 0006310 | biological_process | DNA recombination |
D | 0006325 | biological_process | chromatin organization |
D | 0008270 | molecular_function | zinc ion binding |
D | 0030183 | biological_process | B cell differentiation |
D | 0030217 | biological_process | T cell differentiation |
D | 0033077 | biological_process | T cell differentiation in thymus |
D | 0033085 | biological_process | negative regulation of T cell differentiation in thymus |
D | 0033151 | biological_process | V(D)J recombination |
D | 0035064 | molecular_function | methylated histone binding |
D | 0035091 | molecular_function | phosphatidylinositol binding |
D | 0035265 | biological_process | organ growth |
D | 0042742 | biological_process | defense response to bacterium |
D | 0043325 | molecular_function | phosphatidylinositol-3,4-bisphosphate binding |
D | 0046622 | biological_process | positive regulation of organ growth |
D | 0046872 | molecular_function | metal ion binding |
D | 0080025 | molecular_function | phosphatidylinositol-3,5-bisphosphate binding |
D | 1904155 | biological_process | DN2 thymocyte differentiation |
N | 0003677 | molecular_function | DNA binding |
N | 0005634 | cellular_component | nucleus |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | binding site for residue ZN A 1101 |
Chain | Residue |
A | CYS727 |
A | CYS730 |
A | HIS937 |
A | HIS942 |
site_id | AC2 |
Number of Residues | 3 |
Details | binding site for residue CA A 1102 |
Chain | Residue |
A | ASP600 |
A | GLY601 |
F | DT31 |
site_id | AC3 |
Number of Residues | 4 |
Details | binding site for residue ZN C 1101 |
Chain | Residue |
C | HIS937 |
C | HIS942 |
C | CYS727 |
C | CYS730 |
site_id | AC4 |
Number of Residues | 4 |
Details | binding site for residue CA C 1102 |
Chain | Residue |
C | ASP600 |
C | GLY601 |
G | DG41 |
G | DT42 |
Functional Information from PROSITE/UniProt
site_id | PS00353 |
Number of Residues | 12 |
Details | HMG_BOX_1 HMG box A DNA-binding domain signature. FSKKCsERWKTM |
Chain | Residue | Details |
N | PHE41-MET52 |
site_id | PS00435 |
Number of Residues | 11 |
Details | PEROXIDASE_1 Peroxidases proximal heme-ligand signature. DTVYILGGHSL |
Chain | Residue | Details |
D | ASP214-LEU224 |
site_id | PS00518 |
Number of Residues | 10 |
Details | ZF_RING_1 Zinc finger RING-type signature. CkHlFCriCI |
Chain | Residue | Details |
A | CYS305-ILE314 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 136 |
Details | ZN_FING: PHD-type; atypical |
Chain | Residue | Details |
D | TRP416-ILE484 | |
B | TRP416-ILE484 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15964836, ECO:0000269|PubMed:18025461 |
Chain | Residue | Details |
D | CYS419 | |
B | CYS423 | |
B | CYS446 | |
B | HIS452 | |
B | HIS455 | |
B | CYS458 | |
B | CYS478 | |
B | HIS481 | |
D | CYS423 | |
D | CYS446 | |
D | HIS452 | |
D | HIS455 | |
D | CYS458 | |
D | CYS478 | |
D | HIS481 | |
B | CYS419 |
site_id | SWS_FT_FI3 |
Number of Residues | 134 |
Details | DNA_BIND: NBD => ECO:0000255|PROSITE-ProRule:PRU00820 |
Chain | Residue | Details |
A | GLY389-GLN456 | |
C | GLY389-GLN456 |
site_id | SWS_FT_FI4 |
Number of Residues | 22 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9228952 |
Chain | Residue | Details |
A | CYS266 | |
A | CYS325 | |
A | CYS328 | |
C | CYS266 | |
C | HIS270 | |
C | CYS290 | |
C | CYS293 | |
C | HIS295 | |
C | CYS305 | |
C | HIS307 | |
C | CYS310 | |
A | HIS270 | |
C | CYS313 | |
C | CYS325 | |
C | CYS328 | |
A | CYS290 | |
A | CYS293 | |
A | HIS295 | |
A | CYS305 | |
A | HIS307 | |
A | CYS310 | |
A | CYS313 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01101, ECO:0000269|PubMed:9228952 |
Chain | Residue | Details |
A | CYS355 | |
A | CYS360 | |
A | HIS372 | |
A | HIS376 | |
C | CYS355 | |
C | CYS360 | |
C | HIS372 | |
C | HIS376 |
site_id | SWS_FT_FI6 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305 |
Chain | Residue | Details |
A | ASP600 | |
A | ASP708 | |
A | GLN962 | |
C | ASP600 | |
C | ASP708 | |
C | GLN962 | |
N | LYS127 | |
N | LYS128 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | SITE: Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage site |
Chain | Residue | Details |
A | TRP893 | |
C | TRP893 |
site_id | SWS_FT_FI8 |
Number of Residues | 1 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
N | LYS30 |
site_id | SWS_FT_FI9 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
N | SER35 |
site_id | SWS_FT_FI10 |
Number of Residues | 3 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P63158 |
Chain | Residue | Details |
N | LYS43 | |
N | LYS90 | |
N | LYS141 |
site_id | SWS_FT_FI11 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
Chain | Residue | Details |
N | SER100 |
site_id | SWS_FT_FI12 |
Number of Residues | 1 |
Details | MOD_RES: Cysteine sulfonic acid (-SO3H) => ECO:0000250|UniProtKB:P63159 |
Chain | Residue | Details |
N | CYS106 |
site_id | SWS_FT_FI13 |
Number of Residues | 5 |
Details | CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-?) => ECO:0000269|PubMed:29618516 |
Chain | Residue | Details |
N | LYS28 | |
N | LYS43 | |
N | LYS44 | |
N | LYS68 |