5IFE
Crystal structure of the human SF3b core complex
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000124 | cellular_component | SAGA complex |
A | 0000375 | biological_process | RNA splicing, via transesterification reactions |
A | 0000398 | biological_process | mRNA splicing, via spliceosome |
A | 0003676 | molecular_function | nucleic acid binding |
A | 0005515 | molecular_function | protein binding |
A | 0005634 | cellular_component | nucleus |
A | 0005654 | cellular_component | nucleoplasm |
A | 0005681 | cellular_component | spliceosomal complex |
A | 0005684 | cellular_component | U2-type spliceosomal complex |
A | 0005686 | cellular_component | U2 snRNP |
A | 0005689 | cellular_component | U12-type spliceosomal complex |
A | 0005730 | cellular_component | nucleolus |
A | 0006282 | biological_process | regulation of DNA repair |
A | 0006397 | biological_process | mRNA processing |
A | 0008380 | biological_process | RNA splicing |
A | 0030620 | molecular_function | U2 snRNA binding |
A | 0042177 | biological_process | negative regulation of protein catabolic process |
A | 0043484 | biological_process | regulation of RNA splicing |
A | 0044877 | molecular_function | protein-containing complex binding |
A | 0045893 | biological_process | positive regulation of DNA-templated transcription |
A | 0071005 | cellular_component | U2-type precatalytic spliceosome |
A | 0071013 | cellular_component | catalytic step 2 spliceosome |
A | 1903241 | biological_process | U2-type prespliceosome assembly |
B | 0000124 | cellular_component | SAGA complex |
B | 0000398 | biological_process | mRNA splicing, via spliceosome |
B | 0003723 | molecular_function | RNA binding |
B | 0005515 | molecular_function | protein binding |
B | 0005634 | cellular_component | nucleus |
B | 0005654 | cellular_component | nucleoplasm |
B | 0005681 | cellular_component | spliceosomal complex |
B | 0005684 | cellular_component | U2-type spliceosomal complex |
B | 0005686 | cellular_component | U2 snRNP |
B | 0005689 | cellular_component | U12-type spliceosomal complex |
B | 0006282 | biological_process | regulation of DNA repair |
B | 0006397 | biological_process | mRNA processing |
B | 0008380 | biological_process | RNA splicing |
B | 0043484 | biological_process | regulation of RNA splicing |
B | 0045893 | biological_process | positive regulation of DNA-templated transcription |
B | 0071005 | cellular_component | U2-type precatalytic spliceosome |
B | 0071011 | cellular_component | precatalytic spliceosome |
B | 1903241 | biological_process | U2-type prespliceosome assembly |
B | 1990935 | molecular_function | splicing factor binding |
C | 0000245 | biological_process | spliceosomal complex assembly |
C | 0000375 | biological_process | RNA splicing, via transesterification reactions |
C | 0000398 | biological_process | mRNA splicing, via spliceosome |
C | 0003723 | molecular_function | RNA binding |
C | 0003729 | molecular_function | mRNA binding |
C | 0005515 | molecular_function | protein binding |
C | 0005634 | cellular_component | nucleus |
C | 0005654 | cellular_component | nucleoplasm |
C | 0005681 | cellular_component | spliceosomal complex |
C | 0005684 | cellular_component | U2-type spliceosomal complex |
C | 0005686 | cellular_component | U2 snRNP |
C | 0005689 | cellular_component | U12-type spliceosomal complex |
C | 0005730 | cellular_component | nucleolus |
C | 0006338 | biological_process | chromatin remodeling |
C | 0006397 | biological_process | mRNA processing |
C | 0008380 | biological_process | RNA splicing |
C | 0016607 | cellular_component | nuclear speck |
C | 0034693 | cellular_component | U11/U12 snRNP |
C | 0045943 | biological_process | positive regulation of transcription by RNA polymerase I |
C | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
C | 0045945 | biological_process | positive regulation of transcription by RNA polymerase III |
C | 0071004 | cellular_component | U2-type prespliceosome |
C | 0071005 | cellular_component | U2-type precatalytic spliceosome |
C | 0071013 | cellular_component | catalytic step 2 spliceosome |
C | 0110016 | cellular_component | B-WICH complex |
C | 1903241 | biological_process | U2-type prespliceosome assembly |
C | 1990935 | molecular_function | splicing factor binding |
D | 0000398 | biological_process | mRNA splicing, via spliceosome |
D | 0003677 | molecular_function | DNA binding |
D | 0003723 | molecular_function | RNA binding |
D | 0005515 | molecular_function | protein binding |
D | 0005634 | cellular_component | nucleus |
D | 0005654 | cellular_component | nucleoplasm |
D | 0005681 | cellular_component | spliceosomal complex |
D | 0005684 | cellular_component | U2-type spliceosomal complex |
D | 0005686 | cellular_component | U2 snRNP |
D | 0005689 | cellular_component | U12-type spliceosomal complex |
D | 0006397 | biological_process | mRNA processing |
D | 0008270 | molecular_function | zinc ion binding |
D | 0008380 | biological_process | RNA splicing |
D | 0016363 | cellular_component | nuclear matrix |
D | 0016607 | cellular_component | nuclear speck |
D | 0045893 | biological_process | positive regulation of DNA-templated transcription |
D | 0046872 | molecular_function | metal ion binding |
D | 0048863 | biological_process | stem cell differentiation |
D | 0071005 | cellular_component | U2-type precatalytic spliceosome |
D | 0071011 | cellular_component | precatalytic spliceosome |
D | 1903241 | biological_process | U2-type prespliceosome assembly |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | binding site for residue ZN D 201 |
Chain | Residue |
D | CYS23 |
D | CYS26 |
D | CYS58 |
D | CYS61 |
site_id | AC2 |
Number of Residues | 4 |
Details | binding site for residue ZN D 202 |
Chain | Residue |
D | CYS11 |
D | CYS46 |
D | CYS49 |
D | CYS85 |
site_id | AC3 |
Number of Residues | 4 |
Details | binding site for residue ZN D 203 |
Chain | Residue |
D | CYS33 |
D | CYS72 |
D | CYS75 |
D | CYS30 |
site_id | AC4 |
Number of Residues | 3 |
Details | binding site for residue K A 1301 |
Chain | Residue |
A | VAL610 |
A | ASN612 |
A | GLN636 |
Functional Information from PROSITE/UniProt
site_id | PS00290 |
Number of Residues | 7 |
Details | IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. FVCSATH |
Chain | Residue | Details |
A | PHE287-HIS293 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 5 |
Details | SITE: Interaction with SF3B5 => ECO:0000269|PubMed:27720643 |
Chain | Residue | Details |
A | GLY284 | |
D | CYS72 | |
D | CYS75 | |
D | CYS85 | |
A | GLU306 | |
A | GLU352 | |
A | ARG429 | |
A | ASN916 | |
D | CYS46 | |
D | CYS49 | |
D | CYS58 | |
D | CYS61 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | SITE: Interaction with SF3B1 => ECO:0000269|PubMed:27720643 |
Chain | Residue | Details |
A | ASN988 | |
A | LYS1171 |
site_id | SWS_FT_FI3 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | SER156 | |
C | CYS677 | |
C | GLU1205 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | THR1200 | |
C | THR235 | |
C | THR426 |
site_id | SWS_FT_FI5 |
Number of Residues | 1 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
D | LYS3 |
site_id | SWS_FT_FI6 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
D | SER94 | |
C | LYS554 | |
C | LYS562 |
site_id | SWS_FT_FI7 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17924679, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR142 |
site_id | SWS_FT_FI8 |
Number of Residues | 1 |
Details | MOD_RES: Citrulline => ECO:0000250 |
Chain | Residue | Details |
C | ARG157 |
site_id | SWS_FT_FI9 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | SER194 |
site_id | SWS_FT_FI10 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231 |
Chain | Residue | Details |
C | THR203 |
site_id | SWS_FT_FI11 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR207 |
site_id | SWS_FT_FI12 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | THR211 |
site_id | SWS_FT_FI13 |
Number of Residues | 1 |
Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:Q99NB9 |
Chain | Residue | Details |
C | LYS214 |
site_id | SWS_FT_FI14 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:17924679, ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR223 |
site_id | SWS_FT_FI15 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR227 |
site_id | SWS_FT_FI16 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q99NB9 |
Chain | Residue | Details |
C | SER229 |
site_id | SWS_FT_FI17 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:12105215 |
Chain | Residue | Details |
C | THR244 |
site_id | SWS_FT_FI18 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0000305|PubMed:12105215 |
Chain | Residue | Details |
C | THR248 |
site_id | SWS_FT_FI19 |
Number of Residues | 5 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | THR257 | |
C | THR261 | |
C | THR278 | |
C | THR303 | |
C | THR313 |
site_id | SWS_FT_FI20 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | THR267 |
site_id | SWS_FT_FI21 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | THR273 |
site_id | SWS_FT_FI22 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | SER287 |
site_id | SWS_FT_FI23 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR296 |
site_id | SWS_FT_FI24 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17081983 |
Chain | Residue | Details |
C | THR299 |
site_id | SWS_FT_FI25 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | SER322 |
site_id | SWS_FT_FI26 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR326 |
site_id | SWS_FT_FI27 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231 |
Chain | Residue | Details |
C | THR328 |
site_id | SWS_FT_FI28 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | SER332 |
site_id | SWS_FT_FI29 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692 |
Chain | Residue | Details |
C | THR341 |
site_id | SWS_FT_FI30 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
Chain | Residue | Details |
C | SER344 |
site_id | SWS_FT_FI31 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692 |
Chain | Residue | Details |
C | SER349 |
site_id | SWS_FT_FI32 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR350 | |
C | THR436 |
site_id | SWS_FT_FI33 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR354 |
site_id | SWS_FT_FI34 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | SER400 |
site_id | SWS_FT_FI35 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine; by DYRK1A => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
C | THR434 |
site_id | SWS_FT_FI36 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
C | SER488 |
site_id | SWS_FT_FI37 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
Chain | Residue | Details |
C | LYS214 |
site_id | SWS_FT_FI38 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
Chain | Residue | Details |
C | LYS430 |
site_id | SWS_FT_FI39 |
Number of Residues | 1 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25114211, ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733 |
Chain | Residue | Details |
C | LYS413 |