7ZSA
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042682 | 3001330 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042684 | 3001330 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042684 | 3001330 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | N-terminal heterodimerisation domain of RBP7 (RpoE) | 8044252 | 3001137 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | Nucleic acid-binding proteins | 8044251 | 3000135 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8093392 | 3002702 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8041967 | 3002702 | SCOP2B (2022-06-29) |
J | SCOP2B Superfamily | RNA polymerase subunit RPB10 | 8042692 | 3001213 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042694 | 3001655 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | RNA polymerase subunits | 8042695 | 3001823 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | Zinc beta-ribbon | 8082617 | 3001238 | SCOP2B (2022-06-29) |
O | SCOP2B Superfamily | TATA-box binding protein-like | 8036833 | 3000705 | SCOP2B (2022-06-29) |
O | SCOP2B Superfamily | TATA-box binding protein-like | 8036831 | 3000705 | SCOP2B (2022-06-29) |
S [auth U] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) alpha-helical domain | 8036834 | 3001887 | SCOP2B (2022-06-29) |
S [auth U] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) beta-barrel domain | 8036836 | 3001281 | SCOP2B (2022-06-29) |
T [auth V] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) alpha-helical domain | 8036837 | 3001887 | SCOP2B (2022-06-29) |
T [auth V] | SCOP2B Superfamily | Transcription factor IIA (TFIIA) beta-barrel domain | 8036838 | 3001281 | SCOP2B (2022-06-29) |
X [auth 1] | SCOP2B Superfamily | PH domain-like | 8034115 | 3000134 | SCOP2B (2022-06-29) |
BA [auth 5] | SCOP2B Superfamily | TFB5-like | 8086592 | 3000733 | SCOP2B (2022-06-29) |
CA [auth 6] | SCOP2B Superfamily | vWA-like | 8057085 | 3000832 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8042687 | 3001500 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042685 | 3001655 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042685 | 3001655 | SCOP2B (2022-06-29) |
IA [auth e] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
EA [auth a] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
FA [auth b] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
JA [auth f] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
GA [auth c] | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2022-06-29) |
KA [auth g] | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2022-06-29) |
LA [auth h] | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2022-06-29) |
HA [auth d] | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | RPB5-like RNA polymerase subunit | 8035939 | 3001722 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | Eukaryotic RPB5 N-terminal domain | 8044454 | 3000444 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | RPB6/omega subunit-like | 8042688 | 3000189 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Zinc beta-ribbon | 8042689 | 3001238 | SCOP2B (2022-06-29) |
I | SCOP2B Superfamily | Zinc beta-ribbon | 8042690 | 3001238 | 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 | PF00623 | e7zsaA4 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00623 | ECOD (1.6) |
A | PF00623 | e7zsaA7 | A: a+b two layers | X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase | F: PF00623 | ECOD (1.6) |
A | PF04990 | e7zsaA2 | A: a+b two layers | X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | F: PF04990 | ECOD (1.6) |
A | F_UNCLASSIFIED | e7zsaA9 | A: a+b two layers | X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | F: F_UNCLASSIFIED | ECOD (1.6) |
A | PF04997 | e7zsaA6 | A: a+b complex topology | X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology) | H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology) | T: N-terminal domain in RNA-polymerase beta-prime subunit | F: PF04997 | ECOD (1.6) |
A | PF04998 | e7zsaA1 | A: a+b complex topology | X: central helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: central helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: central helical domain in RNA-polymerase beta-prime subunit | F: PF04998 | ECOD (1.6) |
A | PF04992 | e7zsaA3 | A: a+b complex topology | X: helical domain in yeast RNA-polymerases | H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology) | T: third helical domain in yeast RNA-polymerase II beta-prime subunit | F: PF04992 | ECOD (1.6) |
A | PF04998,PF05000 | e7zsaA5 | A: a+b complex topology | X: second helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: second helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: second helical domain in RNA-polymerase beta-prime subunit | F: PF04998,PF05000 | ECOD (1.6) |
A | PF04983 | e7zsaA8 | A: a+b complex topology | X: first helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: first helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: first helical domain in RNA-polymerase beta-prime subunit | F: PF04983 | ECOD (1.6) |
B | PF00562 | e7zsaB6 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00562 | ECOD (1.6) |
B | PF00562 | e7zsaB3 | 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) |
B | PF04563,PF04565 | e7zsaB5 | 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) |
B | PF04561 | e7zsaB7 | 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) |
B | PF00562,PF04567 | e7zsaB1 | 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) |
B | PF00562,PF04560 | e7zsaB2 | 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) |
B | PF04566 | e7zsaB4 | 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) |
G | PF00575 | e7zsaG1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF00575 | ECOD (1.6) |
G | PF03876 | e7zsaG2 | 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) |
H | PF03870 | e7zsaH1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF03870 | ECOD (1.6) |
J | PF01194 | e7zsaJ1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: PF01194 | ECOD (1.6) |
K | PF13656 | e7zsaK1 | 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) |
L | PF03604 | e7zsaL1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF03604 | ECOD (1.6) |
M | PF00382 | e7zsaM2 | A: alpha arrays | X: HTH | H: HTH | T: Cyclin-like | F: PF00382 | ECOD (1.6) |
M | PF08271 | e7zsaM1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF08271 | ECOD (1.6) |
O | PF00352 | e7zsaO1 | 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) |
S [auth U] | PF03153 | e7zsaU2 | 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) |
S [auth U] | PF03153 | e7zsaU1 | 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) |
T [auth V] | PF02751 | e7zsaV1 | 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) |
T [auth V] | PF02268 | e7zsaV2 | 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) |
W [auth 0] | PF06777 | e7zsa03 | 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) |
W [auth 0] | PF06733 | e7zsa02 | 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) |
W [auth 0] | PF13307 | e7zsa01 | 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) |
Z [auth 3] | PF17121 | e7zsa31 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: RING/U-box | F: PF17121 | ECOD (1.6) |
Z [auth 3] | PF06391 | e7zsa32 | 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) |
AA [auth 4] | PF03850 | e7zsa42 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: PF03850 | ECOD (1.6) |
AA [auth 4] | F_UNCLASSIFIED | e7zsa41 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
BA [auth 5] | PF06331 | e7zsa51 | A: a+b complex topology | X: TFB5-related (From Topology) | H: TFB5-related (From Topology) | T: TFB5-related | F: PF06331 | ECOD (1.6) |
C | PF01193 | e7zsaC2 | 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) |
C | PF01000 | e7zsaC1 | 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) |
IA [auth e] | PF00125 | e7zsae1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
EA [auth a] | PF00125 | e7zsaa1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
FA [auth b] | PF15511 | e7zsab1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
JA [auth f] | PF15511 | e7zsaf1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
GA [auth c] | PF00125,PF16211 | e7zsac1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
KA [auth g] | PF00125,PF16211 | e7zsag1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
LA [auth h] | PF00125 | e7zsah1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
HA [auth d] | PF00125 | e7zsad1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
D | PF03874 | e7zsaD1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PF03874 | ECOD (1.6) |
E | PF01191 | e7zsaE1 | 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) |
E | PF03871 | e7zsaE2 | 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) |
F | PF01192 | e7zsaF1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: PF01192 | ECOD (1.6) |
I | PF01096 | e7zsaI2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01096 | ECOD (1.6) |
I | PF02150 | e7zsaI1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF02150 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family | |
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 | |
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 | |
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 | |
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 | |
PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family | |
PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | - | Domain | |
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 | |
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 | |
PF03604 | DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD) | DNA directed RNA polymerase, 7 kDa subunit | - | Domain | |
PF00382 | Transcription factor TFIIB repeat (TFIIB) | Transcription factor TFIIB repeat | - | Domain | |
PF00352 | Transcription factor TFIID (or TATA-binding protein, TBP) (TBP) | Transcription factor TFIID (or TATA-binding protein, TBP) | - | Domain | |
Q [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 |
Q [auth R] | PF17683 | TFIIF, beta subunit N-terminus (TFIIF_beta_N) | TFIIF, beta subunit N-terminus | - | Family |
T [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 |
T [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 |
U [auth W] | PF02002 | TFIIE alpha subunit (TFIIE_alpha) | TFIIE alpha subunit | - | Family |
V [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 |
V [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 |
W [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 |
W [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 |
W [auth 0] | PF06733 | DEAD_2 (DEAD_2) | DEAD_2 | - | Family |
X [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 |
X [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 |
Y [auth 2] | PF03849 | Transcription factor Tfb2 (Tfb2) | Transcription factor Tfb2 | - | Family |
Y [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 |
Z [auth 3] | PF17121 | Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_5) | Zinc finger, C3HC4 type (RING finger) | - | Domain |
Z [auth 3] | PF06391 | CDK-activating kinase assembly factor MAT1 (MAT1) | CDK-activating kinase assembly factor MAT1 | - | Family |
AA [auth 4] | PF03850 | Transcription factor Tfb4 (Tfb4) | Transcription factor Tfb4 | This family appears to be distantly related to the VWA domain. | Domain |
BA [auth 5] | PF06331 | Transcription factor TFIIH complex subunit Tfb5 (Tfb5) | Transcription factor TFIIH complex subunit Tfb5 | - | Family |
CA [auth 6] | PF04056 | Ssl1-like (Ssl1) | Ssl1-like | - | Family |
CA [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 |
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 | |
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 | |
DA [auth 7] | PF04851 | Type III restriction enzyme, res subunit (ResIII) | Type III restriction enzyme, res subunit | - | Family |
EA [auth a], IA [auth e] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
FA [auth b], JA [auth f] | 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 |
GA [auth c], KA [auth g] | PF16211 | C-terminus of histone H2A (Histone_H2A_C) | C-terminus of histone H2A | - | Family |
GA [auth c], KA [auth g] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
HA [auth d], LA [auth h] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family | |
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 | |
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 | |
PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family | |
PF02150 | RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD) | RNA polymerases M/15 Kd subunit | - | Domain | |
PF01096 | Transcription factor S-II (TFIIS) (TFIIS_C) | Transcription factor S-II (TFIIS) | - | Domain |