6J50
RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation)
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
J | SCOP2B Superfamily | RNA polymerase subunit RPB10 | 8063366 | 3001213 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8080724 | 3001655 | SCOP2B (2022-06-29) |
T [auth c] | SCOP2B Superfamily | Core histone-like | 8039342 | 3001387 | SCOP2B (2022-06-29) |
X [auth g] | SCOP2B Superfamily | Core histone-like | 8039342 | 3001387 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | RNA polymerase subunits | 8080893 | 3001823 | SCOP2B (2022-06-29) |
R [auth a] | SCOP2B Superfamily | Core histone-like | 8070527 | 3001387 | SCOP2B (2022-06-29) |
V [auth e] | SCOP2B Superfamily | Core histone-like | 8070527 | 3001387 | SCOP2B (2022-06-29) |
W [auth f] | SCOP2B Superfamily | Core histone-like | 8070545 | 3001387 | SCOP2B (2022-06-29) |
S [auth b] | SCOP2B Superfamily | Core histone-like | 8070545 | 3001387 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | HRDC-like | 8078369 | 3000132 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | RPB6/omega subunit-like | 8078373 | 3000189 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8078385 | 3002702 | SCOP2B (2022-06-29) |
H | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8093395 | 3002702 | 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 | e6j50A6 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00623 | ECOD (1.6) |
A | PF00623 | e6j50A4 | 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 | e6j50A9 | 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 | e6j50A7 | 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 | e6j50A3 | 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 | e6j50A8 | 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 | e6j50A5 | 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 | e6j50A1 | 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 | e6j50A2 | 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) |
E | PF01191 | e6j50E2 | 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 | e6j50E1 | 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) |
J | PF01194 | e6j50J1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: PF01194 | ECOD (1.6) |
K | PF13656 | e6j50K1 | 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) |
Q [auth W] | PF00467 | e6j50W1 | A: beta barrels | X: SH3 | H: SH3 | T: SH3 | F: PF00467 | ECOD (1.6) |
Q [auth W] | PF03439 | e6j50W2 | A: a+b two layers | X: Alpha-beta plaits | H: N-utilization substance G protein NusG, N-terminal domain (From Topology) | T: N-utilization substance G protein NusG, N-terminal domain | F: PF03439 | ECOD (1.6) |
T [auth c] | PF00125,PF16211 | e6j50c1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
X [auth g] | PF00125,PF16211 | e6j50g1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
L | PF03604 | e6j50L1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF03604 | ECOD (1.6) |
P [auth V] | PF06093 | e6j50V1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF06093 | ECOD (1.6) |
R [auth a] | PF00125 | e6j50a1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
V [auth e] | PF00125 | e6j50e1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
W [auth f] | PF15511 | e6j50f1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
S [auth b] | PF15511 | e6j50b1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
B | PF00562 | e6j50B1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00562 | ECOD (1.6) |
B | PF00562 | e6j50B2 | 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 | e6j50B6 | 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 | e6j50B5 | 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 | e6j50B7 | 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 | e6j50B4 | 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 | e6j50B3 | 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) |
U [auth d] | PF00125 | e6j50d1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
Y [auth h] | PF00125 | e6j50h1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
C | PF01193 | e6j50C2 | 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 | e6j50C1 | 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) |
D | PF03874 | e6j50D1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: PF03874 | ECOD (1.6) |
F | PF01192 | e6j50F1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: PF01192 | ECOD (1.6) |
G | PF00575 | e6j50G2 | 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 | e6j50G1 | 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 | e6j50H1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: PF03870 | ECOD (1.6) |
I | PF01096 | e6j50I1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PF01096 | ECOD (1.6) |
I | PF02150 | e6j50I2 | 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 | |
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 | |
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 | |
Q [auth W] | PF03439 | Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN) | Early transcription elongation factor of RNA pol II, NGN section | - | Family |
Q [auth W] | PF11942 | Spt5 transcription elongation factor, acidic N-terminal (Spt5_N) | Spt5 transcription elongation factor, acidic N-terminal | This is the very acidic N-terminal region of the early transcription elongation factor Spt5 [1]. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical assoc ... | Domain |
Q [auth W] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
T [auth c], X [auth g] | PF16211 | C-terminus of histone H2A (Histone_H2A_C) | C-terminus of histone H2A | - | Family |
T [auth c], X [auth g] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
PF03604 | DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD) | DNA directed RNA polymerase, 7 kDa subunit | - | Domain | |
P [auth V] | PF06093 | Spt4/RpoE2 zinc finger (Spt4) | Spt4/RpoE2 zinc finger | This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via ... | Domain |
R [auth a], V [auth e] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
S [auth b], W [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 |
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 | |
U [auth d], Y [auth h] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | 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 | |
PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family | |
PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family | |
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 | |
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 |