8CEO
Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
J [auth B] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042684 | 3001330 | SCOP2B (2022-06-29) |
J [auth B] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042684 | 3001330 | SCOP2B (2022-06-29) |
K [auth C] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8042687 | 3001500 | SCOP2B (2022-06-29) |
K [auth C] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042685 | 3001655 | SCOP2B (2022-06-29) |
K [auth C] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042685 | 3001655 | SCOP2B (2022-06-29) |
M [auth E] | SCOP2B Superfamily | RPB5-like RNA polymerase subunit | 8035939 | 3001722 | SCOP2B (2022-06-29) |
M [auth E] | SCOP2B Superfamily | Eukaryotic RPB5 N-terminal domain | 8044454 | 3000444 | SCOP2B (2022-06-29) |
N [auth F] | SCOP2B Superfamily | RPB6/omega subunit-like | 8042688 | 3000189 | SCOP2B (2022-06-29) |
O [auth G] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044251 | 3000135 | SCOP2B (2022-06-29) |
O [auth G] | SCOP2B Superfamily | N-terminal heterodimerisation domain of RBP7 (RpoE) | 8044252 | 3001137 | SCOP2B (2022-06-29) |
P [auth H] | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8093392 | 3002702 | SCOP2B (2022-06-29) |
P [auth H] | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8041967 | 3002702 | SCOP2B (2022-06-29) |
Q [auth I] | SCOP2B Superfamily | Zinc beta-ribbon | 8042689 | 3001238 | SCOP2B (2022-06-29) |
Q [auth I] | SCOP2B Superfamily | Zinc beta-ribbon | 8042690 | 3001238 | SCOP2B (2022-06-29) |
R [auth J] | SCOP2B Superfamily | RNA polymerase subunit RPB10 | 8042692 | 3001213 | SCOP2B (2022-06-29) |
S [auth K] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042694 | 3001655 | SCOP2B (2022-06-29) |
T [auth L] | SCOP2B Superfamily | RNA polymerase subunits | 8042695 | 3001823 | SCOP2B (2022-06-29) |
U [auth M] | SCOP2B Superfamily | Zinc beta-ribbon | 8082617 | 3001238 | SCOP2B (2022-06-29) |
AA [auth U] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) beta-barrel domain | 8107122 | 3001281 | SCOP2B (2022-06-29) |
BA [auth V] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) beta-barrel domain | 8107118 | 3001281 | SCOP2B (2022-06-29) |
JA [auth f] | SCOP2B Superfamily | CYTH-like phosphatases | 8091513 | 3001426 | SCOP2B (2022-06-29) |
KA [auth g] | SCOP2B Superfamily | Mediator subcomplex-like | 8051778 | 3001613 | SCOP2B (2022-06-29) |
UA [auth r] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
YA [auth v] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
VA [auth s] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
ZA [auth w] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
AB [auth x] | SCOP2B Superfamily | Core histone-like | 8067126 | 3001387 | SCOP2B (2022-06-29) |
WA [auth t] | SCOP2B Superfamily | Core histone-like | 8067126 | 3001387 | SCOP2B (2022-06-29) |
I [auth A] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042682 | 3001330 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth 0] | PF06777 | e8ceo03 | A: a+b two layers | X: XPD arch domain (From Topology) | H: XPD arch domain (From Topology) | T: XPD arch domain | F: PF06777 | ECOD (1.6) |
A [auth 0] | PF06733 | e8ceo02 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: PF06733 | ECOD (1.6) |
A [auth 0] | PF13307 | e8ceo01 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: PF13307 | ECOD (1.6) |
J [auth B] | PF00562 | e8ceoB2 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00562 | ECOD (1.6) |
J [auth B] | PF00562 | e8ceoB3 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: PF00562 | ECOD (1.6) |
J [auth B] | PF04563,PF04565 | e8ceoB7 | A: a+b complex topology | X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: PF04563,PF04565 | ECOD (1.6) |
J [auth B] | PF04561 | e8ceoB1 | A: a+b complex topology | X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: insertion domain in beta subunit of DNA dependent RNA-polymerase | F: PF04561 | ECOD (1.6) |
J [auth B] | PF00562,PF04567 | e8ceoB6 | A: a+b complex topology | X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: barrel domain in beta subunit of DNA dependent RNA-polymerase | F: PF00562,PF04567 | ECOD (1.6) |
J [auth B] | PF00562,PF04560 | e8ceoB4 | A: a+b complex topology | X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: PF00562,PF04560 | ECOD (1.6) |
J [auth B] | PF04566 | e8ceoB5 | A: a+b complex topology | X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | T: inserted a+b domain in yeast RNA polymerase beta subunit | F: PF04566 | ECOD (1.6) |
K [auth C] | PF01193 | e8ceoC2 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: PF01193 | ECOD (1.6) |
K [auth C] | PF01000 | e8ceoC1 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Insert subdomain of RNA polymerase alpha subunit (From Topology) | T: Insert subdomain of RNA polymerase alpha subunit | F: PF01000 | ECOD (1.6) |
L [auth D] | PF03874 | e8ceoD1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PF03874 | ECOD (1.6) |
M [auth E] | PF01191 | e8ceoE2 | A: a+b two layers | X: RPB5-like RNA polymerase subunit (From Topology) | H: RPB5-like RNA polymerase subunit (From Topology) | T: RPB5-like RNA polymerase subunit | F: PF01191 | ECOD (1.6) |
M [auth E] | PF03871 | e8ceoE1 | A: a/b three-layered sandwiches | X: Restriction endonuclease-like | H: Eukaryotic RPB5 N-terminal domain (From Topology) | T: Eukaryotic RPB5 N-terminal domain | F: PF03871 | ECOD (1.6) |
N [auth F] | PF01192 | e8ceoF1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: PF01192 | ECOD (1.6) |
O [auth G] | PF00575 | e8ceoG1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00575 | ECOD (1.6) |
O [auth G] | PF03876 | e8ceoG2 | A: a+b two layers | X: Dodecin subunit-like | H: Flavin-binding protein dodecin-like (From Topology) | T: Flavin-binding protein dodecin-like | F: PF03876 | ECOD (1.6) |
P [auth H] | PF03870 | e8ceoH1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF03870 | ECOD (1.6) |
Q [auth I] | PF01096 | e8ceoI1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01096 | ECOD (1.6) |
Q [auth I] | PF02150 | e8ceoI2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF02150 | ECOD (1.6) |
R [auth J] | PF01194 | e8ceoJ1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: PF01194 | ECOD (1.6) |
S [auth K] | PF13656 | e8ceoK1 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: PF13656 | ECOD (1.6) |
T [auth L] | PF03604 | e8ceoL1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF03604 | ECOD (1.6) |
U [auth M] | PF00382 | e8ceoM3 | A: alpha arrays | X: HTH | H: HTH | T: Cyclin-like | F: PF00382 | ECOD (1.6) |
U [auth M] | PF08271 | e8ceoM2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF08271 | ECOD (1.6) |
W [auth O] | PF00352 | e8ceoO2 | A: a+b two layers | X: TBP-like | H: TATA-box binding protein-like (From Topology) | T: TATA-box binding protein-like | F: PF00352 | ECOD (1.6) |
AA [auth U] | PF03153 | e8ceoU2 | A: beta duplicates or obligate multimers | X: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | T: Transcription factor IIA (TFIIA), beta-barrel domain | F: PF03153 | ECOD (1.6) |
AA [auth U] | PF03153 | e8ceoU1 | A: alpha duplicates or obligate multimers | X: TFIIA, alpha-helical domain (From Topology) | H: TFIIA, alpha-helical domain (From Topology) | T: TFIIA, alpha-helical domain | F: PF03153 | ECOD (1.6) |
BA [auth V] | PF02751 | e8ceoV2 | A: beta duplicates or obligate multimers | X: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | T: Transcription factor IIA (TFIIA), beta-barrel domain | F: PF02751 | ECOD (1.6) |
BA [auth V] | PF02268 | e8ceoV1 | A: alpha duplicates or obligate multimers | X: TFIIA, alpha-helical domain (From Topology) | H: TFIIA, alpha-helical domain (From Topology) | T: TFIIA, alpha-helical domain | F: PF02268 | ECOD (1.6) |
EA [auth a] | PF04934 | e8ceoa1 | A: extended segments | X: Mediator of RNA polymerase II transcription subunit 6 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 6 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 6 | F: PF04934 | ECOD (1.6) |
FA [auth b] | PF10232 | e8ceob1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription subunit 8 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 8 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 8 | F: PF10232 | ECOD (1.6) |
GA [auth c] | PF10280 | e8ceoc1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription subunit 11 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 11 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 11 | F: PF10280 | ECOD (1.6) |
IA [auth e] | PF09637 | e8ceoe1 | A: a+b complex topology | X: mRNA triphosphatase CET1-related (From Topology) | H: mRNA triphosphatase CET1-related (From Topology) | T: mRNA triphosphatase CET1-related | F: PF09637 | ECOD (1.6) |
JA [auth f] | PF08612 | e8ceof1 | A: a+b complex topology | X: mRNA triphosphatase CET1-related (From Topology) | H: mRNA triphosphatase CET1-related (From Topology) | T: mRNA triphosphatase CET1-related | F: PF08612 | ECOD (1.6) |
KA [auth g] | PF06179 | e8ceog1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription subunit 22 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 22 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 22 | F: PF06179 | ECOD (1.6) |
MA [auth i] | PF05983 | e8ceoi2 | A: alpha duplicates or obligate multimers | X: Mediator hinge subcomplex-like (From Homology) | H: Mediator hinge subcomplex-like | T: MED7 hinge region | F: PF05983 | ECOD (1.6) |
MA [auth i] | PF05983 | e8ceoi1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | H: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | T: Mediator of RNA polymerase II transcription submodule Med7N/31 | F: PF05983 | ECOD (1.6) |
D [auth 3] | PF17121 | e8ceo31 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: RING/U-box | F: PF17121 | ECOD (1.6) |
D [auth 3] | PF06391 | e8ceo32 | A: few secondary structure elements | X: beta-beta-alpha zinc fingers | H: beta-beta-alpha zinc fingers (From Topology) | T: beta-beta-alpha zinc fingers | F: PF06391 | ECOD (1.6) |
RA [auth n] | PF11221 | e8ceon1 | A: alpha duplicates or obligate multimers | X: Mediator hinge subcomplex-like (From Homology) | H: Mediator hinge subcomplex-like | T: RNA polymerase II holoenzyme component SRB7 (MED21) | F: PF11221 | ECOD (1.6) |
SA [auth o] | PF05669 | e8ceoo1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | H: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | T: Mediator of RNA polymerase II transcription submodule Med7N/31 | F: PF05669 | ECOD (1.6) |
UA [auth r] | PF00125 | e8ceor1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
YA [auth v] | PF00125 | e8ceov1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
VA [auth s] | PF15511 | e8ceos1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
ZA [auth w] | PF15511 | e8ceow1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
AB [auth x] | PF00125,PF16211 | e8ceox1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
WA [auth t] | PF00125,PF16211 | e8ceot1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
E [auth 4] | PF03850 | e8ceo41 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03850 | ECOD (1.6) |
E [auth 4] | F_UNCLASSIFIED | e8ceo42 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
BB [auth y] | PF00125 | e8ceoy1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
XA [auth u] | PF00125 | e8ceou1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
F [auth 5] | PF06331 | e8ceo51 | A: a+b complex topology | X: TFB5-related (From Topology) | H: TFB5-related (From Topology) | T: TFB5-related | F: PF06331 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth 0] | PF13307 | Helicase C-terminal domain (Helicase_C_2) | Helicase C-terminal domain | This domain is found at the C-terminus of DEAD-box helicases. | Domain |
A [auth 0] | PF06733 | DEAD_2 (DEAD_2) | DEAD_2 | - | Family |
A [auth 0] | PF06777 | Helical and beta-bridge domain (HBB) | Helical and beta-bridge domain | HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ... | Domain |
J [auth B] | PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ... | Domain |
J [auth B] | PF04560 | RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7) | RNA polymerase Rpb2, domain 7 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ... | Domain |
J [auth B] | PF04565 | RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3) | RNA polymerase Rpb2, domain 3 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ... | Domain |
J [auth B] | PF04566 | RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4) | RNA polymerase Rpb2, domain 4 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ... | Domain |
J [auth B] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
J [auth B] | PF00562 | RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6) | RNA polymerase Rpb2, domain 6 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ... | Domain |
J [auth B] | PF04567 | RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5) | RNA polymerase Rpb2, domain 5 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ... | Domain |
K [auth C] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
K [auth C] | PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain |
L [auth D] | PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family |
M [auth E] | PF01191 | RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C) | RNA polymerase Rpb5, C-terminal domain | The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. | Domain |
M [auth E] | PF03871 | RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N) | RNA polymerase Rpb5, N-terminal domain | Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ... | Domain |
N [auth F] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
O [auth G] | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N) | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ... | Domain |
O [auth G] | PF00575 | S1 RNA binding domain (S1) | S1 RNA binding domain | The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. | Domain |
P [auth H] | PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family |
Q [auth I] | PF02150 | RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD) | RNA polymerases M/15 Kd subunit | - | Domain |
Q [auth I] | PF01096 | Transcription factor S-II (TFIIS) (TFIIS_C) | Transcription factor S-II (TFIIS) | - | Domain |
R [auth J] | PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | - | Domain |
S [auth K] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
S [auth K] | PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
B [auth 1] | PF03909 | BSD domain (BSD) | BSD domain | This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function. | Domain |
B [auth 1] | PF08567 | TFIIH p62 subunit, N-terminal domain (PH_TFIIH) | TFIIH p62 subunit, N-terminal domain | The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision ... | Domain |
T [auth L] | PF03604 | DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD) | DNA directed RNA polymerase, 7 kDa subunit | - | Domain |
U [auth M] | PF00382 | Transcription factor TFIIB repeat (TFIIB) | Transcription factor TFIIB repeat | - | Domain |
W [auth O] | PF00352 | Transcription factor TFIID (or TATA-binding protein, TBP) (TBP) | Transcription factor TFIID (or TATA-binding protein, TBP) | - | Domain |
Y [auth R] | PF02270 | TFIIF, beta subunit HTH domain (TFIIF_beta) | TFIIF, beta subunit HTH domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which ... | Domain |
Y [auth R] | PF17683 | TFIIF, beta subunit N-terminus (TFIIF_beta_N) | TFIIF, beta subunit N-terminus | - | Family |
BA [auth V] | PF02751 | Transcription initiation factor IIA, gamma subunit (TFIIA_gamma_C) | Transcription initiation factor IIA, gamma subunit | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA b ... | Domain |
BA [auth V] | PF02268 | Transcription initiation factor IIA, gamma subunit, helical domain (TFIIA_gamma_N) | Transcription initiation factor IIA, gamma subunit, helical domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA ... | Domain |
CA [auth W] | PF02002 | TFIIE alpha subunit (TFIIE_alpha) | TFIIE alpha subunit | - | Family |
C [auth 2] | PF03849 | Transcription factor Tfb2 (Tfb2) | Transcription factor Tfb2 | - | Family |
C [auth 2] | PF18307 | Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C) | Transcription factor Tfb2 (p52) C-terminal domain | This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ... | Domain |
DA [auth X] | PF18121 | TFA2 Winged helix domain 2 (TFA2_Winged_2) | TFA2 Winged helix domain 2 | This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase [1]. | Domain |
DA [auth X] | PF02186 | TFIIE beta subunit core domain (TFIIE_beta) | TFIIE beta subunit core domain | General transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymer ... | Domain |
EA [auth a] | PF04934 | MED6 mediator sub complex component (Med6) | MED6 mediator sub complex component | - | Family |
FA [auth b] | PF10232 | Mediator of RNA polymerase II transcription complex subunit 8 (Med8) | Mediator of RNA polymerase II transcription complex subunit 8 | - | Family |
GA [auth c] | PF10280 | Mediator complex protein (Med11) | Mediator complex protein | - | Family |
HA [auth d] | PF10156 | Subunit 17 of Mediator complex (Med17) | Subunit 17 of Mediator complex | - | Family |
IA [auth e] | PF09637 | Med18 protein (Med18) | Med18 protein | Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Me ... | Domain |
JA [auth f] | PF08612 | TATA-binding related factor (TRF) of subunit 20 of Mediator complex (Med20) | TATA-binding related factor (TRF) of subunit 20 of Mediator complex | - | Family |
KA [auth g] | PF06179 | Surfeit locus protein 5 subunit 22 of Mediator complex (Med22) | Surfeit locus protein 5 subunit 22 of Mediator complex | - | Family |
LA [auth h] | PF10018 | Vitamin-D-receptor interacting Mediator subunit 4 (Med4) | Vitamin-D-receptor interacting Mediator subunit 4 | - | Family |
MA [auth i] | PF05983 | MED7 protein (Med7) | MED7 protein | - | Family |
D [auth 3] | PF17121 | Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_5) | Zinc finger, C3HC4 type (RING finger) | - | Domain |
D [auth 3] | PF06391 | CDK-activating kinase assembly factor MAT1 (MAT1) | CDK-activating kinase assembly factor MAT1 | - | Family |
NA [auth j] | PF07544 | RNA polymerase II transcription mediator complex subunit 9 (Med9) | RNA polymerase II transcription mediator complex subunit 9 | - | Family |
OA [auth k] | PF09748 | Transcription factor subunit Med10 of Mediator complex (Med10) | Transcription factor subunit Med10 of Mediator complex | - | Family |
PA [auth l] | PF08638 | Mediator complex subunit MED14 (Med14) | Mediator complex subunit MED14 | - | Family |
QA [auth m] | PF08633 | Rox3 mediator complex subunit (Rox3) | Rox3 mediator complex subunit | - | Family |
RA [auth n] | PF11221 | Subunit 21 of Mediator complex (Med21) | Subunit 21 of Mediator complex | - | Family |
SA [auth o] | PF05669 | SOH1 (Med31) | SOH1 | - | Family |
TA [auth p] | PF10744 | Mediator of RNA polymerase II transcription subunit 1 (Med1) | Mediator of RNA polymerase II transcription subunit 1 | Mediator complexes are basic necessities for linking transcriptional regulators to RNA polymerase II. This domain, Med1, is conserved from plants to fungi to humans and forms part of the Med9 submodule of the Srb/Med complex. it is one of three subu ... | Domain |
UA [auth r], YA [auth v] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
VA [auth s], ZA [auth w] | PF15511 | Centromere kinetochore component CENP-T histone fold (CENP-T_C) | Centromere kinetochore component CENP-T histone fold | CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ... | Domain |
AB [auth x], WA [auth t] | PF16211 | C-terminus of histone H2A (Histone_H2A_C) | C-terminus of histone H2A | - | Family |
AB [auth x], WA [auth t] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
E [auth 4] | PF03850 | Transcription factor Tfb4 (Tfb4) | Transcription factor Tfb4 | This family appears to be distantly related to the VWA domain. | Domain |
F [auth 5] | PF06331 | Transcription factor TFIIH complex subunit Tfb5 (Tfb5) | Transcription factor TFIIH complex subunit Tfb5 | - | Family |
G [auth 6] | PF04056 | Ssl1-like (Ssl1) | Ssl1-like | - | Family |
G [auth 6] | PF07975 | TFIIH C1-like domain (C1_4) | TFIIH C1-like domain | The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD ... | Domain |
H [auth 7] | PF04851 | Type III restriction enzyme, res subunit (ResIII) | Type III restriction enzyme, res subunit | - | Family |
I [auth A] | PF00623 | RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2) | RNA polymerase Rpb1, domain 2 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ... | Domain |
I [auth A] | PF04990 | RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7) | RNA polymerase Rpb1, domain 7 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ... | Domain |
I [auth A] | PF05001 | RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R) | RNA polymerase Rpb1 C-terminal repeat | - | Repeat |
I [auth A] | PF05000 | RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4) | RNA polymerase Rpb1, domain 4 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ... | Domain |
I [auth A] | PF04983 | RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3) | RNA polymerase Rpb1, domain 3 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ... | Domain |
I [auth A] | PF04992 | RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6) | RNA polymerase Rpb1, domain 6 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ... | Domain |
I [auth A] | PF04998 | RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5) | RNA polymerase Rpb1, domain 5 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ... | Domain |
I [auth A] | PF04997 | RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1) | RNA polymerase Rpb1, domain 1 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ... | Domain |