9NB1 | pdb_00009nb1

CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilySm-like ribonucleoproteins 8041751 3000419 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilySm-like ribonucleoproteins 8063476 3000419 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilySm-like ribonucleoproteins 8063452 3000419 SCOP2B (2022-06-29)
E [auth G]SCOP2B SuperfamilySm-like ribonucleoproteins 8063468 3000419 SCOP2B (2022-06-29)
F [auth J]SCOP2B SuperfamilyARM repeat-like 8093027 3000116 SCOP2B (2022-06-29)
J [auth B]SCOP2B SuperfamilySm-like ribonucleoproteins 8041747 3000419 SCOP2B (2022-06-29)
L [auth H]SCOP2B SuperfamilyMetallo-hydrolase/oxidoreductase 8034424 3001057 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ABeta-Caspe9nb1A1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
B [auth C]Beta-Caspe9nb1C1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
C [auth E]Beta-Caspe9nb1E1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
D [auth F]Beta-Caspe9nb1F1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
E [auth G]Beta-Caspe9nb1G1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
F [auth J]Beta-Caspe9nb1J1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
J [auth B]Beta-Caspe9nb1B1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
L [auth H]Beta-Caspe9nb1H1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)
M [auth I]Beta-Caspe9nb1I1 A: alpha arraysX: HTHH: HTHT: Three-helical HTHF: Beta-CaspECOD (v295)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
B [auth C]PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
C [auth E]PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
D [auth F]PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
E [auth G]PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
F [auth J]PF11935Symplekin/PTA1 N-terminal (SYMPK_PTA1_N)Symplekin/PTA1 N-terminal- Repeat
J [auth B]PF01423LSM domain (LSM)LSM domainThe LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Domain
L [auth H]PF07521Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)Zn-dependent metallo-hydrolase RNA specificity domain- Motif
L [auth H]PF11718Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term (CPSF73-100_C)Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-termThis is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known. Domain
L [auth H]PF10996Beta-Casp domain (Beta-Casp)Beta-Casp domainThe beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1]. Domain
L [auth H]PF00753Metallo-beta-lactamase superfamily (Lactamase_B)Metallo-beta-lactamase superfamilyDomain
M [auth I]PF07521Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)Zn-dependent metallo-hydrolase RNA specificity domain- Motif
M [auth I]PF16661Metallo-beta-lactamase superfamily domain (Lactamase_B_6)Metallo-beta-lactamase superfamily domainThis family is part of the metallo-beta-lactamase superfamily. Domain
M [auth I]PF13299Cleavage and polyadenylation factor 2 C-terminal (CPSF100_C)Cleavage and polyadenylation factor 2 C-terminal- Family
M [auth I]PF10996Beta-Casp domain (Beta-Casp)Beta-Casp domainThe beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1]. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Small nuclear ribonucleoprotein Sm D3
B [auth C]U7 snRNA-associated Sm-like protein LSm10
C [auth E]Small nuclear ribonucleoprotein E
D [auth F]Small nuclear ribonucleoprotein F
E [auth G]Small nuclear ribonucleoprotein G
F [auth J]Symplekin-
G [auth K]CstF77---
H [auth Y]modified H2a pre-mRNA---
I [auth Z]U7 snRNA---
J [auth B]Small nuclear ribonucleoprotein-associated proteins B and B'
K [auth D]U7 snRNA-associated Sm-like protein LSm11---
L [auth H]Cleavage and polyadenylation specificity factor subunit 3
M [auth I]Cleavage and polyadenylation specificity factor subunit 2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR027141Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3Family
IPR034099Small nuclear ribonucleoprotein Sm D3Family
IPR001163Sm domain, eukaryotic/archaea-typeDomain
IPR047575Sm domainDomain
IPR010920LSM domain superfamilyHomologous Superfamily
B [auth C]IPR001163Sm domain, eukaryotic/archaea-typeDomain
B [auth C]IPR052840U7 snRNA-associated Sm-likeFamily
B [auth C]IPR047575Sm domainDomain
B [auth C]IPR010920LSM domain superfamilyHomologous Superfamily
C [auth E]IPR027078Small nuclear ribonucleoprotein EFamily
C [auth E]IPR001163Sm domain, eukaryotic/archaea-typeDomain
C [auth E]IPR047575Sm domainDomain
C [auth E]IPR010920LSM domain superfamilyHomologous Superfamily
D [auth F]IPR016487Sm-like protein Lsm6/SmFFamily
D [auth F]IPR034100Small nuclear ribonucleoprotein FFamily
D [auth F]IPR001163Sm domain, eukaryotic/archaea-typeDomain
D [auth F]IPR047575Sm domainDomain
D [auth F]IPR010920LSM domain superfamilyHomologous Superfamily
E [auth G]IPR044641Sm-like protein Lsm7/SmGFamily
E [auth G]IPR034098Small nuclear ribonucleoprotein GFamily
E [auth G]IPR001163Sm domain, eukaryotic/archaea-typeDomain
E [auth G]IPR047575Sm domainDomain
E [auth G]IPR010920LSM domain superfamilyHomologous Superfamily
F [auth J]IPR022075Symplekin C-terminalDomain
F [auth J]IPR016024Armadillo-type foldHomologous Superfamily
F [auth J]IPR021850Symplekin/Pta1Family
F [auth J]IPR032460Symplekin/Pta1, N-terminalDomain
F [auth J]IPR011989Armadillo-like helicalHomologous Superfamily
J [auth B]IPR001163Sm domain, eukaryotic/archaea-typeDomain
J [auth B]IPR017131Small ribonucleoprotein associated, SmB/SmNFamily
J [auth B]IPR047575Sm domainDomain
J [auth B]IPR010920LSM domain superfamilyHomologous Superfamily
L [auth H]IPR001279Metallo-beta-lactamaseDomain
L [auth H]IPR022712Beta-Casp domainDomain
L [auth H]IPR050698RNA Processing Metallo-Beta-LactamaseFamily
L [auth H]IPR021718Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-termDomain
L [auth H]IPR011108Zn-dependent metallo-hydrolase, RNA specificity domainDomain
L [auth H]IPR036866Ribonuclease Z/Hydroxyacylglutathione hydrolase-likeHomologous Superfamily
M [auth I]IPR001279Metallo-beta-lactamaseDomain
M [auth I]IPR022712Beta-Casp domainDomain
M [auth I]IPR027075Cleavage and polyadenylation specificity factor subunit 2Family
M [auth I]IPR011108Zn-dependent metallo-hydrolase, RNA specificity domainDomain
M [auth I]IPR036866Ribonuclease Z/Hydroxyacylglutathione hydrolase-likeHomologous Superfamily
M [auth I]IPR025069Cleavage and polyadenylation specificity factor 2, C-terminalDomain
M [auth I]IPR035639CPSF2, metallo-hydrolase domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
P62318
B [auth C]Q969L4
C [auth E]P62304
D [auth F]P62306
E [auth G]P62308
F [auth J]Q92797
J [auth B]P14678
L [auth H]Q9UKF6
M [auth I]Q9P2I0