8YJB | pdb_00008yjb

Cryo-EM structure of the human DSS1-INTAC complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
G [auth P]SCOP2B SuperfamilyARM repeat-like 8038568 3000116 SCOP2B (2022-06-29)
H [auth Q]SCOP2B SuperfamilyMetallo-dependent phosphatases 8039778 3001067 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth K]PF21386Integrator IntS11, C-terminal domain (IntS11_C)Integrator IntS11, C-terminal domainIntS11 is the catalytic component of integrator complex (INT), which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS11 which interacts with the C-te ...IntS11 is the catalytic component of integrator complex (INT), which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS11 which interacts with the C-terminal of IntS9 (Pfam:PF21382), which is a crucial interaction for the role of INT in snRNA 3'-end processing [1,2]. IntS11 is responsible of the endonuclease activity of INT [1-3].
Domain
C [auth K]PF07521Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)Zn-dependent metallo-hydrolase RNA specificity domain- Motif
C [auth K]PF16661Metallo-beta-lactamase superfamily domain (Lactamase_B_6)Metallo-beta-lactamase superfamily domainThis family is part of the metallo-beta-lactamase superfamily. Domain
C [auth K]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
D [auth B]PF14750Integrator complex subunit 2 (INTS2)Integrator complex subunit 2- Family
E [auth D]PF13646HEAT repeats (HEAT_2)HEAT repeats- Repeat
E [auth D]PF25458Integrator subunit 4 family C-terminal Ig-like domain (INTS4_C)Integrator subunit 4 family C-terminal Ig-like domainThis entry represents the C-terminal domain of Integrator subunit 4 (INTS4). The domain has been structurally identified near the INTS9 beta-CASP domain but is poorly resolved in current structures, suggesting flexibility. INTS4 is a component of the ...This entry represents the C-terminal domain of Integrator subunit 4 (INTS4). The domain has been structurally identified near the INTS9 beta-CASP domain but is poorly resolved in current structures, suggesting flexibility. INTS4 is a component of the Integrator complex which plays essential roles in snRNA 3' end processing and transcription termination. The specific function of the C-terminal domain remains to be determined.
Domain
E [auth D]PF20168Sister chromatid cohesion protein PDS5 protein (PDS5)Sister chromatid cohesion protein PDS5 protein- Repeat
E [auth D]PF24493INTS4 8 helical bundle domain (INTS4_8HBD)INTS4 8 helical bundle domainThis domain is found in the homologs of Integrator complex subunit 4 (INTS4). INTS4 along with INTS9 and INTS11 constitute the Integrator cleavage module, which contains endonuclease activity and resembles the cleavage module of the cleavage and pol ...This domain is found in the homologs of Integrator complex subunit 4 (INTS4). INTS4 along with INTS9 and INTS11 constitute the Integrator cleavage module, which contains endonuclease activity and resembles the cleavage module of the cleavage and polyadenylation specific factor required for 3' processing of mRNA transcripts. The domain represented by this entry makes extensive contacts with INTS7 and stabilize the beta-CASP domain of INTS9 in the cleavage module [1,2]. It folds into an eight alpha-helical bundle.
Domain
G [auth P]PF02985HEAT repeat (HEAT)HEAT repeat- Repeat
H [auth Q]PF00149Calcineurin-like phosphoesterase (Metallophos)Calcineurin-like phosphoesteraseThis family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.
Domain
I [auth A]PF22928Integrator complex subunit 1, R4 domain (INTS1_R4)Integrator complex subunit 1, R4 domain- Repeat
I [auth A]PF22927Integrator complex subunit 1, R3 domain (INT1_R3)Integrator complex subunit 1, R3 domain- Repeat
I [auth A]PF22929Integrator complex subunit 1, INTS2-binding domain (INTS1_INTS2-bd)Integrator complex subunit 1, INTS2-binding domain- Repeat
K [auth F]PF13519von Willebrand factor type A domain (VWA_2)von Willebrand factor type A domainDomain
K [auth F]PF25462INTS6 beta-barrel domain (Beta-barrel_INTS6)INTS6 beta-barrel domainThis entry represents a domain found in the human Integrator complex subunit 6 (INTS6) and related proteins, including its paralogue Integrator complex subunit 6-like (INTS6L). INTS6 is a component of the Integrator (INT) complex, a complex that is i ...This entry represents a domain found in the human Integrator complex subunit 6 (INTS6) and related proteins, including its paralogue Integrator complex subunit 6-like (INTS6L). INTS6 is a component of the Integrator (INT) complex, a complex that is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. INTS6 and other subunits bind to and position PP2A phosphatase to dephosphorylate the C-terminal domain of Pol II subunit RPB1 [1,2]. In the inactive closed conformation of the INT-PP2A complex, INTS6 blocks the PP2A phosphatase active site. The domain represented by this entry folds into a beta-barrel structure with topological similarity to SPOC domains.
Domain
F [auth G]PF24436Integrator complex subunit 7, N-terminal (INTS7_N)Integrator complex subunit 7, N-terminal- Repeat
F [auth G]PF24437Integrator complex subunit 7 helical bundle (INTS7_HB)Integrator complex subunit 7 helical bundleIntegrator complex subunit 7 (INTS7) is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the large ...Integrator complex subunit 7 (INTS7) is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing [1]. This entry represents the helical bundle (HB) of INTS7, localised between the superhelical alpha-solenoid (Pfam:PF24436) and the C-terminal beta- sandwich (Pfam:PF22965) [2]. INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex [2].
Domain
F [auth G]PF22965Integrator complex subunit 7, C-terminal domain (INTS7_C)Integrator complex subunit 7, C-terminal domainThis entry represents a C-terminal domain found in the Integrator complex subunit 7 (INTS7). INTS7 is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The inte ...This entry represents a C-terminal domain found in the Integrator complex subunit 7 (INTS7). INTS7 is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing [1].
Domain
B [auth I]PF21382Integrator IntS9, C-terminal domain (IntS9_C)Integrator IntS9, C-terminal domainIntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS9 which interacts with the C-terminal of IntS1 ...IntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS9 which interacts with the C-terminal of IntS11 (responsible for endonuclease activity of INT), a crucial interaction for the role of INT in snRNA 3'-end processing [1,2].
Domain
B [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
B [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
L [auth H]PF25756INTS8, TPR repeats (TPR_INTS8)INTS8, TPR repeats- Repeat
J [auth E]PF14838Integrator complex subunit 5 C-terminus (INTS5_C)Integrator complex subunit 5 C-terminus- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 0]26S proteasome complex subunit DSS1
C [auth K]Integrator complex subunit 11
D [auth B]Integrator complex subunit 2-
E [auth D]Integrator complex subunit 4
G [auth P]Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
H [auth Q]Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
I [auth A]Integrator complex subunit 1-
K [auth F]Integrator complex subunit 6
F [auth G]Integrator complex subunit 7-
B [auth I]Integrator complex subunit 9-
L [auth H]Integrator complex subunit 8-
J [auth E]Integrator complex subunit 5-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth 0]IPR007834DSS1/SEM1Family
C [auth K]IPR001279Metallo-beta-lactamaseDomain
C [auth K]IPR022712Beta-Casp domainDomain
C [auth K]IPR050698RNA Processing Metallo-Beta-LactamaseFamily
C [auth K]IPR041897Integrator complex subunit 11, MBL-foldDomain
C [auth K]IPR048662Integrator complex subunit 11, C-terminal domainDomain
C [auth K]IPR011108Zn-dependent metallo-hydrolase, RNA specificity domainDomain
C [auth K]IPR036866Ribonuclease Z/Hydroxyacylglutathione hydrolase-likeHomologous Superfamily
D [auth B]IPR026236Integrator complex subunit 2, metazoaFamily
D [auth B]IPR029321Integrator complex subunit 2Family
E [auth D]IPR016024Armadillo-type foldHomologous Superfamily
E [auth D]IPR011989Armadillo-like helicalHomologous Superfamily
E [auth D]IPR057412Integrator complex subunit 4/Protein SIEL, C-terminal Ig-like domainDomain
E [auth D]IPR056235INTS4, 8 helical bundle domainDomain
G [auth P]IPR054573Phosphatase PP2A regulatory subunit A/Splicing factor 3B subunit 1-like, HEAT repeatDomain
G [auth P]IPR016024Armadillo-type foldHomologous Superfamily
G [auth P]IPR021133HEAT, type 2Repeat
G [auth P]IPR011989Armadillo-like helicalHomologous Superfamily
G [auth P]IPR055231PIK3R4-like, middle domainDomain
G [auth P]IPR051023Protein Phosphatase 2A Regulatory Subunit AFamily
G [auth P]IPR000357HEAT repeatRepeat
H [auth Q]IPR047129Serine/Threonine protein phosphatase PP2A-likeFamily
H [auth Q]IPR029052Metallo-dependent phosphatase-likeHomologous Superfamily
H [auth Q]IPR004843Calcineurin-like, phosphoesterase domainDomain
H [auth Q]IPR006186Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphataseDomain
I [auth A]IPR016024Armadillo-type foldHomologous Superfamily
I [auth A]IPR053964Integrator complex subunit 1, R3 domainDomain
I [auth A]IPR053966Integrator complex subunit 1, INTS2-binding domainDomain
I [auth A]IPR022145Integrator complex subunit 1, RPB2-binding domainDomain
I [auth A]IPR053965Integrator complex subunit 1, R4 domainDomain
I [auth A]IPR038902Integrator complex subunit 1Family
K [auth F]IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
K [auth F]IPR057413Integrator complex subunit 6-like, beta-barrel domainDomain
K [auth F]IPR002035von Willebrand factor, type ADomain
K [auth F]IPR029307INTS6/SAGE1/DDX26B/CT45, C-terminalDomain
K [auth F]IPR051113Integrator complex subunit 6Family
F [auth G]IPR056517Integrator complex subunit 7, helical bundleDomain
F [auth G]IPR016024Armadillo-type foldHomologous Superfamily
F [auth G]IPR033060Integrator complex subunit 7Family
F [auth G]IPR054519Integrator complex subunit 7, C-terminal domainDomain
F [auth G]IPR056516Integrator complex subunit 7, N-terminalDomain
B [auth I]IPR027074Integrator complex subunit 9Family
B [auth I]IPR001279Metallo-beta-lactamaseDomain
B [auth I]IPR022712Beta-Casp domainDomain
B [auth I]IPR036866Ribonuclease Z/Hydroxyacylglutathione hydrolase-likeHomologous Superfamily
B [auth I]IPR048660Integrator complex subunit 9-like, C-terminal domainDomain
L [auth H]IPR038751INTS8Family
L [auth H]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
L [auth H]IPR057980Integrator complex subunit 8, TPR repeatsDomain
J [auth E]IPR040316Integrator complex subunit 5Family
J [auth E]IPR029445Integrator complex subunit 5, N-terminalDomain
J [auth E]IPR029444Integrator complex subunit 5, C-terminalDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth 0]PharosP60896
C [auth K]PharosQ5TA45
D [auth B]PharosQ9H0H0
E [auth D]PharosQ96HW7
G [auth P]PharosP30153
H [auth Q]PharosP67775
I [auth A]PharosQ8N201
K [auth F]PharosQ9UL03
F [auth G]PharosQ9NVH2
B [auth I]PharosQ9NV88
L [auth H]PharosQ75QN2
J [auth E]PharosQ6P9B9