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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9ZED

Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2)

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0000245biological_processspliceosomal complex assembly
A0000381biological_processregulation of alternative mRNA splicing, via spliceosome
A0003677molecular_functionDNA binding
A0003723molecular_functionRNA binding
A0003729molecular_functionmRNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005681cellular_componentspliceosomal complex
A0006396biological_processRNA processing
A0008285biological_processnegative regulation of cell population proliferation
A0043065biological_processpositive regulation of apoptotic process
A10000387biological_processspliceosomal snRNP assembly
A10000389biological_processmRNA 3'-splice site recognition
A10000398biological_processmRNA splicing, via spliceosome
A10003723molecular_functionRNA binding
A10005515molecular_functionprotein binding
A10005634cellular_componentnucleus
A10005654cellular_componentnucleoplasm
A10005681cellular_componentspliceosomal complex
A10005684cellular_componentU2-type spliceosomal complex
A10005686cellular_componentU2 snRNP
A10006397biological_processmRNA processing
A10016607cellular_componentnuclear speck
A10071004cellular_componentU2-type prespliceosome
A10071005cellular_componentU2-type precatalytic spliceosome
A10071006cellular_componentU2-type catalytic step 1 spliceosome
A10071011cellular_componentprecatalytic spliceosome
A10071013cellular_componentcatalytic step 2 spliceosome
A11903241biological_processU2-type prespliceosome assembly
A20000245biological_processspliceosomal complex assembly
A20000387biological_processspliceosomal snRNP assembly
A20000389biological_processmRNA 3'-splice site recognition
A20000398biological_processmRNA splicing, via spliceosome
A20003723molecular_functionRNA binding
A20005515molecular_functionprotein binding
A20005634cellular_componentnucleus
A20005654cellular_componentnucleoplasm
A20005681cellular_componentspliceosomal complex
A20005684cellular_componentU2-type spliceosomal complex
A20005686cellular_componentU2 snRNP
A20006397biological_processmRNA processing
A20010976biological_processpositive regulation of neuron projection development
A20016607cellular_componentnuclear speck
A20071004cellular_componentU2-type prespliceosome
A20071005cellular_componentU2-type precatalytic spliceosome
A20071006cellular_componentU2-type catalytic step 1 spliceosome
A20071011cellular_componentprecatalytic spliceosome
A20071013cellular_componentcatalytic step 2 spliceosome
A21903241biological_processU2-type prespliceosome assembly
A30000375biological_processRNA splicing, via transesterification reactions
A30000387biological_processspliceosomal snRNP assembly
A30000389biological_processmRNA 3'-splice site recognition
A30000398biological_processmRNA splicing, via spliceosome
A30003723molecular_functionRNA binding
A30005515molecular_functionprotein binding
A30005634cellular_componentnucleus
A30005654cellular_componentnucleoplasm
A30005681cellular_componentspliceosomal complex
A30005684cellular_componentU2-type spliceosomal complex
A30005686cellular_componentU2 snRNP
A30006397biological_processmRNA processing
A30016607cellular_componentnuclear speck
A30071005cellular_componentU2-type precatalytic spliceosome
A30071006cellular_componentU2-type catalytic step 1 spliceosome
A30071011cellular_componentprecatalytic spliceosome
A30071013cellular_componentcatalytic step 2 spliceosome
A31903241biological_processU2-type prespliceosome assembly
B10000245biological_processspliceosomal complex assembly
B10000375biological_processRNA splicing, via transesterification reactions
B10000387biological_processspliceosomal snRNP assembly
B10000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B10000398biological_processmRNA splicing, via spliceosome
B10000785cellular_componentchromatin
B10003723molecular_functionRNA binding
B10003729molecular_functionmRNA binding
B10005515molecular_functionprotein binding
B10005634cellular_componentnucleus
B10005654cellular_componentnucleoplasm
B10005681cellular_componentspliceosomal complex
B10005684cellular_componentU2-type spliceosomal complex
B10005686cellular_componentU2 snRNP
B10005689cellular_componentU12-type spliceosomal complex
B10005730cellular_componentnucleolus
B10006338biological_processchromatin remodeling
B10008380biological_processRNA splicing
B10016607cellular_componentnuclear speck
B10031981cellular_componentnuclear lumen
B10034693cellular_componentU11/U12 snRNP
B10036002molecular_functionpre-mRNA binding
B10045292biological_processmRNA cis splicing, via spliceosome
B10045943biological_processpositive regulation of transcription by RNA polymerase I
B10045944biological_processpositive regulation of transcription by RNA polymerase II
B10045945biological_processpositive regulation of transcription by RNA polymerase III
B10071004cellular_componentU2-type prespliceosome
B10071005cellular_componentU2-type precatalytic spliceosome
B10071006cellular_componentU2-type catalytic step 1 spliceosome
B10071011cellular_componentprecatalytic spliceosome
B10071013cellular_componentcatalytic step 2 spliceosome
B10071016cellular_componentU12-type precatalytic spliceosome
B10071018cellular_componentU12-type catalytic step 2 spliceosome
B10110016cellular_componentB-WICH complex
B11903241biological_processU2-type prespliceosome assembly
B11990935molecular_functionsplicing factor binding
B20000387biological_processspliceosomal snRNP assembly
B20000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B20000398biological_processmRNA splicing, via spliceosome
B20003723molecular_functionRNA binding
B20005515molecular_functionprotein binding
B20005634cellular_componentnucleus
B20005654cellular_componentnucleoplasm
B20005681cellular_componentspliceosomal complex
B20005684cellular_componentU2-type spliceosomal complex
B20005686cellular_componentU2 snRNP
B20005689cellular_componentU12-type spliceosomal complex
B20006397biological_processmRNA processing
B20008380biological_processRNA splicing
B20016607cellular_componentnuclear speck
B20034693cellular_componentU11/U12 snRNP
B20071005cellular_componentU2-type precatalytic spliceosome
B20071006cellular_componentU2-type catalytic step 1 spliceosome
B20071011cellular_componentprecatalytic spliceosome
B20071013cellular_componentcatalytic step 2 spliceosome
B20071016cellular_componentU12-type precatalytic spliceosome
B20071018cellular_componentU12-type catalytic step 2 spliceosome
B21903241biological_processU2-type prespliceosome assembly
B30000124cellular_componentSAGA complex
B30000375biological_processRNA splicing, via transesterification reactions
B30000387biological_processspliceosomal snRNP assembly
B30000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B30000398biological_processmRNA splicing, via spliceosome
B30005515molecular_functionprotein binding
B30005634cellular_componentnucleus
B30005654cellular_componentnucleoplasm
B30005681cellular_componentspliceosomal complex
B30005684cellular_componentU2-type spliceosomal complex
B30005686cellular_componentU2 snRNP
B30005689cellular_componentU12-type spliceosomal complex
B30005730cellular_componentnucleolus
B30006282biological_processregulation of DNA repair
B30008380biological_processRNA splicing
B30030620molecular_functionU2 snRNA binding
B30034693cellular_componentU11/U12 snRNP
B30042177biological_processnegative regulation of protein catabolic process
B30043484biological_processregulation of RNA splicing
B30044877molecular_functionprotein-containing complex binding
B30045893biological_processpositive regulation of DNA-templated transcription
B30071005cellular_componentU2-type precatalytic spliceosome
B30071006cellular_componentU2-type catalytic step 1 spliceosome
B30071011cellular_componentprecatalytic spliceosome
B30071013cellular_componentcatalytic step 2 spliceosome
B30071016cellular_componentU12-type precatalytic spliceosome
B30071018cellular_componentU12-type catalytic step 2 spliceosome
B31903241biological_processU2-type prespliceosome assembly
B40000375biological_processRNA splicing, via transesterification reactions
B40000387biological_processspliceosomal snRNP assembly
B40000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B40000398biological_processmRNA splicing, via spliceosome
B40003723molecular_functionRNA binding
B40005515molecular_functionprotein binding
B40005634cellular_componentnucleus
B40005654cellular_componentnucleoplasm
B40005681cellular_componentspliceosomal complex
B40005684cellular_componentU2-type spliceosomal complex
B40005686cellular_componentU2 snRNP
B40005689cellular_componentU12-type spliceosomal complex
B40006397biological_processmRNA processing
B40008380biological_processRNA splicing
B40034693cellular_componentU11/U12 snRNP
B40071005cellular_componentU2-type precatalytic spliceosome
B40071006cellular_componentU2-type catalytic step 1 spliceosome
B40071011cellular_componentprecatalytic spliceosome
B40071016cellular_componentU12-type precatalytic spliceosome
B40071018cellular_componentU12-type catalytic step 2 spliceosome
B41903241biological_processU2-type prespliceosome assembly
B41990935molecular_functionsplicing factor binding
B50000124cellular_componentSAGA complex
B50000387biological_processspliceosomal snRNP assembly
B50000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B50000398biological_processmRNA splicing, via spliceosome
B50003723molecular_functionRNA binding
B50005515molecular_functionprotein binding
B50005634cellular_componentnucleus
B50005654cellular_componentnucleoplasm
B50005681cellular_componentspliceosomal complex
B50005684cellular_componentU2-type spliceosomal complex
B50005686cellular_componentU2 snRNP
B50005689cellular_componentU12-type spliceosomal complex
B50006282biological_processregulation of DNA repair
B50034693cellular_componentU11/U12 snRNP
B50043484biological_processregulation of RNA splicing
B50045893biological_processpositive regulation of DNA-templated transcription
B50071005cellular_componentU2-type precatalytic spliceosome
B50071006cellular_componentU2-type catalytic step 1 spliceosome
B50071011cellular_componentprecatalytic spliceosome
B50071016cellular_componentU12-type precatalytic spliceosome
B50071018cellular_componentU12-type catalytic step 2 spliceosome
B51903241biological_processU2-type prespliceosome assembly
B51990935molecular_functionsplicing factor binding
B60000387biological_processspliceosomal snRNP assembly
B60000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
B60000398biological_processmRNA splicing, via spliceosome
B60003723molecular_functionRNA binding
B60003729molecular_functionmRNA binding
B60005515molecular_functionprotein binding
B60005634cellular_componentnucleus
B60005654cellular_componentnucleoplasm
B60005681cellular_componentspliceosomal complex
B60005684cellular_componentU2-type spliceosomal complex
B60005686cellular_componentU2 snRNP
B60005689cellular_componentU12-type spliceosomal complex
B60034693cellular_componentU11/U12 snRNP
B60071006cellular_componentU2-type catalytic step 1 spliceosome
B60071011cellular_componentprecatalytic spliceosome
B60071016cellular_componentU12-type precatalytic spliceosome
B60071018cellular_componentU12-type catalytic step 2 spliceosome
B61903241biological_processU2-type prespliceosome assembly
H0000387biological_processspliceosomal snRNP assembly
H0000388biological_processspliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
H0000398biological_processmRNA splicing, via spliceosome
H0003723molecular_functionRNA binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005681cellular_componentspliceosomal complex
H0005684cellular_componentU2-type spliceosomal complex
H0005686cellular_componentU2 snRNP
H0005689cellular_componentU12-type spliceosomal complex
H0008270molecular_functionzinc ion binding
H0016363cellular_componentnuclear matrix
H0016607cellular_componentnuclear speck
H0045893biological_processpositive regulation of DNA-templated transcription
H0048863biological_processstem cell differentiation
H0071005cellular_componentU2-type precatalytic spliceosome
H0071006cellular_componentU2-type catalytic step 1 spliceosome
H0071011cellular_componentprecatalytic spliceosome
H0071013cellular_componentcatalytic step 2 spliceosome
H0071016cellular_componentU12-type precatalytic spliceosome
H0071018cellular_componentU12-type catalytic step 2 spliceosome
H1903241biological_processU2-type prespliceosome assembly
Functional Information from PROSITE/UniProt
site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. FVCSATH
ChainResidueDetails
B3PHE287-HIS293
site_idPS01358
Number of Residues20
DetailsZF_RANBP2_1 Zinc finger RanBP2-type signature. WlCnk..CclnNfrkrlkCfrC
ChainResidueDetails
ATRP185-CYS204
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues61
DetailsZinc finger: {"description":"Matrin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00130","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues3
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues39
DetailsRepeat: {"description":"HEAT 1"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues34
DetailsRepeat: {"description":"HEAT 2"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues37
DetailsRepeat: {"description":"HEAT 3"}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues34
DetailsRepeat: {"description":"HEAT 4"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues38
DetailsRepeat: {"description":"HEAT 5"}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues38
DetailsRepeat: {"description":"HEAT 6"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues38
DetailsRepeat: {"description":"HEAT 7"}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues38
DetailsRepeat: {"description":"HEAT 8"}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues38
DetailsRepeat: {"description":"HEAT 9"}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues38
DetailsRepeat: {"description":"HEAT 10"}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues38
DetailsRepeat: {"description":"HEAT 11"}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues39
DetailsRegion: {"description":"Interaction with SF3B14"}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues4
DetailsRegion: {"description":"Interaction with PHF5A","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues56
DetailsRegion: {"description":"Interaction with SF3B3 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues7
DetailsSite: {"description":"Interaction with RNA","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues1
DetailsSite: {"description":"Interaction with PHF5A","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues4
DetailsSite: {"description":"Interaction with SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI22
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":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues5
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25114211","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25755297","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues1
DetailsModified residue: {"description":"Symmetric dimethylarginine; by PRMT9; alternate","evidences":[{"source":"PubMed","id":"25737013","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues1
DetailsModified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"24129315","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues3
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues37
DetailsRegion: {"description":"Interaction with PHF5A, SF3B1 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues56
DetailsRegion: {"description":"Interaction with SF3B1 and SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues21
DetailsRegion: {"description":"Interaction with SF3B1","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues23
DetailsRegion: {"description":"Interaction with SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI32
Number of Residues5
DetailsSite: {"description":"Interaction with SF3B5","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI33
Number of Residues2
DetailsSite: {"description":"Interaction with SF3B1","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI34
Number of Residues1
DetailsModified residue: {"description":"N-acetylalanine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"DEC-2008","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Lilla S.","von Kriegsheim A.","Lempens A.","Kolch W."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI35
Number of Residues1
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI36
Number of Residues77
DetailsRegion: {"description":"Interaction with SF3B1 and SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI37
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17525332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI38
Number of Residues75
DetailsDomain: {"description":"RRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00176","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI39
Number of Residues13
DetailsRegion: {"description":"Interaction with pre-mRNA branch site"}
ChainResidueDetails
site_idSWS_FT_FI40
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI41
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25755297","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI42
Number of Residues3
DetailsRegion: {"description":"Interaction with SF3B3","evidences":[{"source":"PubMed","id":"27720643","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI43
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"28541300","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5IFE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SYB","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI44
Number of Residues1
DetailsModified residue: {"description":"N-acetylalanine","evidences":[{"source":"UniProtKB","id":"P83870","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

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PDB entries from 2026-05-27

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