Function and Biology

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome

EC 2.7.7.6: DNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • C RNA formation factors
  • C ribonucleic acid formation factors
  • DNA-dependent RNA nucleotidyltransferase
  • DNA-dependent RNA polymerase
  • DNA-dependent ribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid-dependent ribonucleic acid polymerase
  • RNA nucleotidyltransferase
  • RNA nucleotidyltransferase (DNA-directed)
  • RNA polymerase
  • RNA polymerase I
  • RNA polymerase II
  • RNA polymerase III
  • RNA transcriptase
  • Ribonucleate nucleotidyltransferase
  • Ribonucleate polymerase
  • Ribonucleic acid nucleotidyltransferase
  • Ribonucleic acid polymerase
  • Ribonucleic acid transcriptase
  • Ribonucleic polymerase
  • Ribonucleic transcriptase
  • Transcriptase

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF05001
Domain description: RNA polymerase Rpb1 C-terminal repeat
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 15 copies of Pfam domain PF05001 (RNA polymerase Rpb1 C-terminal repeat ) in DNA-directed RNA polymerase subunit. Showing 15 copies in chain A (this domain is out of the observed residue ranges!).

PF00125
Domain description: Core histone H2A/H2B/H3/H4
Occurring in:
  1. Histone H3.3
  2. Histone H2A type 1-B/E
  3. Histone H2B type 1-J
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H3.3. Showing 1 copy in chain S [auth a].
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H2A type 1-B/E. Showing 1 copy in chain Y [auth g].
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H2B type 1-J. Showing 1 copy in chain V [auth d].

PF16211
Domain description: C-terminus of histone H2A
Occurring in:
  1. Histone H2A type 1-B/E
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF16211 (C-terminus of histone H2A) in Histone H2A type 1-B/E. Showing 1 copy in chain Y [auth g].

PF15511
Domain description: Centromere kinetochore component CENP-T histone fold
Occurring in:
  1. Histone H4
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF15511 (Centromere kinetochore component CENP-T histone fold) in Histone H4. Showing 1 copy in chain T [auth b].

PF00467
Domain description: KOW motif
Occurring in:
  1. Transcription elongation factor SPT5
The deposited structure of PDB entry 6ir9 contains 2 copies of Pfam domain PF00467 (KOW motif) in Transcription elongation factor SPT5. Showing 2 copies in chain R [auth W] (some of the copies are out of the observed residue ranges!).

PF12815
Domain description: Spt5 C-terminal nonapeptide repeat binding Spt4
Occurring in:
  1. Transcription elongation factor SPT5
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF12815 (Spt5 C-terminal nonapeptide repeat binding Spt4) in Transcription elongation factor SPT5. Showing 1 copy in chain R [auth W] (this domain is out of the observed residue ranges!).

PF03439
Domain description: Early transcription elongation factor of RNA pol II, NGN section
Occurring in:
  1. Transcription elongation factor SPT5
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03439 (Early transcription elongation factor of RNA pol II, NGN section) in Transcription elongation factor SPT5. Showing 1 copy in chain R [auth W].

PF11942
Domain description: Spt5 transcription elongation factor, acidic N-terminal
Occurring in:
  1. Transcription elongation factor SPT5
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF11942 (Spt5 transcription elongation factor, acidic N-terminal) in Transcription elongation factor SPT5. Showing 1 copy in chain R [auth W].

PF06093
Domain description: Spt4/RpoE2 zinc finger
Occurring in:
  1. Transcription elongation factor SPT4
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF06093 (Spt4/RpoE2 zinc finger) in Transcription elongation factor SPT4. Showing 1 copy in chain Q [auth V].

PF05129
Domain description: Transcription elongation factor Elf1 like
Occurring in:
  1. Transcription elongation factor 1 homolog
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF05129 (Transcription elongation factor Elf1 like) in Transcription elongation factor 1 homolog. Showing 1 copy in chain P [auth M].

PF03604
Domain description: DNA directed RNA polymerase, 7 kDa subunit
Occurring in:
  1. RNA polymerase subunit ABC10-alpha
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03604 (DNA directed RNA polymerase, 7 kDa subunit) in RNA polymerase subunit ABC10-alpha. Showing 1 copy in chain L.

PF13656
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF13656 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein. Showing 1 copy in chain K.

PF01194
Domain description: RNA polymerases N / 8 kDa subunit
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC5
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01194 (RNA polymerases N / 8 kDa subunit) in RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III. Showing 1 copy in chain J.

PF01096
Domain description: Transcription factor S-II (TFIIS)
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01096 (Transcription factor S-II (TFIIS)) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain I.

PF02150
Domain description: RNA polymerases M/15 Kd subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF02150 (RNA polymerases M/15 Kd subunit) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain I.

PF03870
Domain description: RNA polymerase Rpb8
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC3
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03870 (RNA polymerase Rpb8) in DNA-directed RNA polymerases I, II, and III subunit RPABC3. Showing 1 copy in chain H.

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF00575 (S1 RNA binding domain) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.

PF03876
Domain description: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03876 (SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.

PF01192
Domain description: RNA polymerase Rpb6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01192 (RNA polymerase Rpb6 ) in RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III. Showing 1 copy in chain F.

PF01191
Domain description: RNA polymerase Rpb5, C-terminal domain
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01191 (RNA polymerase Rpb5, C-terminal domain) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.

PF03871
Domain description: RNA polymerase Rpb5, N-terminal domain
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03871 (RNA polymerase Rpb5, N-terminal domain) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.

PF03874
Domain description: RNA polymerase Rpb4
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF03874 (RNA polymerase Rpb4) in RNA polymerase Rpb4/RPC9 core domain-containing protein. Showing 1 copy in chain D.

PF01000
Domain description: RNA polymerase Rpb3/RpoA insert domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01000 (RNA polymerase Rpb3/RpoA insert domain) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.

PF01193
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01193 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF01193 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein. Showing 1 copy in chain K.

PF04560
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04560 (RNA polymerase Rpb2, domain 7) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF00562
Domain description: RNA polymerase Rpb2, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF00562 (RNA polymerase Rpb2, domain 6) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04567
Domain description: RNA polymerase Rpb2, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04567 (RNA polymerase Rpb2, domain 5) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04566
Domain description: RNA polymerase Rpb2, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04566 (RNA polymerase Rpb2, domain 4) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04565
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04565 (RNA polymerase Rpb2, domain 3) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04561
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04561 (RNA polymerase Rpb2, domain 2) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04563
Domain description: RNA polymerase beta subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04563 (RNA polymerase beta subunit) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain B.

PF04990
Domain description: RNA polymerase Rpb1, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04990 (RNA polymerase Rpb1, domain 7) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF04992
Domain description: RNA polymerase Rpb1, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04992 (RNA polymerase Rpb1, domain 6) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF04998
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04998 (RNA polymerase Rpb1, domain 5) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF05000
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF05000 (RNA polymerase Rpb1, domain 4) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF04983
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04983 (RNA polymerase Rpb1, domain 3) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF00623
Domain description: RNA polymerase Rpb1, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF00623 (RNA polymerase Rpb1, domain 2) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

PF04997
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of Pfam domain PF04997 (RNA polymerase Rpb1, domain 1) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR000164
Domain description: Histone H3/CENP-A
Occurring in:
  1. Histone H3.3
IPR000684
Domain description: RNA polymerase II, heptapeptide repeat, eukaryotic
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR000558
Domain description: Histone H2B
Occurring in:
  1. Histone H2B type 1-J
IPR002119
Domain description: Histone H2A
Occurring in:
  1. Histone H2A type 1-B/E
IPR001951
Domain description: Histone H4
Occurring in:
  1. Histone H4
IPR009072
Domain description: Histone-fold
Occurring in:
  1. Histone H3.3
  2. Histone H4
  3. Histone H2A type 1-B/E
  4. Histone H2B type 1-J
IPR007125
Domain description: Histone H2A/H2B/H3
Occurring in:
  1. Histone H3.3
  2. Histone H2A type 1-B/E
  3. Histone H2B type 1-J
IPR005824
Domain description: KOW
Occurring in:
  1. Transcription elongation factor SPT5
IPR000268
Domain description: DNA-directed RNA polymerase subunit RPABC5/Rpb10
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC5
IPR012340
Domain description: Nucleic acid-binding, OB-fold
Occurring in:
  1. DNA-directed RNA polymerase subunit
  2. DNA-directed RNA polymerases I, II, and III subunit RPABC3
IPR014722
Domain description: Large ribosomal subunit protein uL2, domain 2
Occurring in:
  1. Transcription elongation factor SPT5
IPR001222
Domain description: Zinc finger, TFIIS-type
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR005570
Domain description: DNA-directed RNA polymerases I, II, and III subunit RPABC3
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC3
IPR014381
Domain description: DNA-directed RNA polymerase subunit Rpo5/Rpb5
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR032454
Domain description: Histone H2A, C-terminal domain
Occurring in:
  1. Histone H2A type 1-B/E
IPR032458
Domain description: Histone H2A conserved site
Occurring in:
  1. Histone H2A type 1-B/E
IPR035425
Domain description: CENP-T/Histone H4, histone fold
Occurring in:
  1. Histone H4
IPR004823
Domain description: TATA box binding protein associated factor (TAF), histone-like fold domain
Occurring in:
  1. Histone H4
IPR019809
Domain description: Histone H4, conserved site
Occurring in:
  1. Histone H4
IPR022800
Domain description: Spt4/RpoE2 zinc finger
Occurring in:
  1. Transcription elongation factor SPT4
IPR009287
Domain description: Transcription initiation Spt4
Occurring in:
  1. Transcription elongation factor SPT4
IPR007808
Domain description: Transcription elongation factor 1
Occurring in:
  1. Transcription elongation factor 1 homolog
IPR006591
Domain description: RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4
Occurring in:
  1. RNA polymerase subunit ABC10-alpha
IPR029040
Domain description: RNA polymerase subunit RPABC4/transcription elongation factor Spt4
Occurring in:
  1. RNA polymerase subunit ABC10-alpha
  2. Transcription elongation factor SPT4
IPR001529
Domain description: DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbon
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR012164
Domain description: DNA-directed RNA polymerase subunit/transcription factor S
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR003029
Domain description: S1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR036898
Domain description: RNA polymerase Rpb7-like, N-terminal domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR006110
Domain description: RNA polymerase, subunit omega/Rpo6/RPB6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR036161
Domain description: RPB6/omega subunit-like superfamily
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR006111
Domain description: Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR035913
Domain description: RPB5-like RNA polymerase subunit superfamily
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR036710
Domain description: RNA polymerase Rpb5, N-terminal domain superfamily
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR036643
Domain description: DNA-directed RNA polymerase, insert domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR011263
Domain description: DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR015712
Domain description: DNA-directed RNA polymerase, subunit 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR044893
Domain description: RNA polymerase Rpb1, clamp domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR041978
Domain description: Spt5, KOW domain repeat 5
Occurring in:
  1. Transcription elongation factor SPT5
IPR041977
Domain description: Spt5, KOW domain repeat 4
Occurring in:
  1. Transcription elongation factor SPT5
IPR041976
Domain description: Spt5, KOW domain repeat 3
Occurring in:
  1. Transcription elongation factor SPT5
IPR008991
Domain description: Translation protein SH3-like domain superfamily
Occurring in:
  1. Transcription elongation factor SPT5
IPR041975
Domain description: Spt5, KOW domain repeat 2
Occurring in:
  1. Transcription elongation factor SPT5
IPR041973
Domain description: Spt5, KOW domain repeat 1
Occurring in:
  1. Transcription elongation factor SPT5
IPR039385
Domain description: NGN domain, eukaryotic
Occurring in:
  1. Transcription elongation factor SPT5
IPR005100
Domain description: NGN domain
Occurring in:
  1. Transcription elongation factor SPT5
IPR036735
Domain description: NusG, N-terminal domain superfamily
Occurring in:
  1. Transcription elongation factor SPT5
IPR022581
Domain description: Spt5 transcription elongation factor, N-terminal
Occurring in:
  1. Transcription elongation factor SPT5
IPR039659
Domain description: Transcription elongation factor SPT5
Occurring in:
  1. Transcription elongation factor SPT5
IPR017071
Domain description: Transcription elongation factor Spt5, eukaryote
Occurring in:
  1. Transcription elongation factor SPT5
IPR038510
Domain description: Spt4 superfamily
Occurring in:
  1. Transcription elongation factor SPT4
IPR038567
Domain description: Transcription elongation factor 1 superfamily
Occurring in:
  1. Transcription elongation factor 1 homolog
IPR039747
Domain description: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Occurring in:
  1. RNA polymerase subunit ABC10-alpha
IPR008193
Domain description: DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR009025
Domain description: DNA-directed RNA polymerase, RBP11-like dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR022905
Domain description: DNA-directed RNA polymerase subunit Rpo11-like
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR037685
Domain description: RNA polymerase RBP11
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR020789
Domain description: RNA polymerases, subunit N, zinc binding site
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC5
IPR023580
Domain description: RNA polymerase subunit RPB10
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC5
IPR034012
Domain description: Pol II subunit B9, C-terminal zinc ribbon
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR019761
Domain description: DNA-directed RNA polymerase M, 15kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR005576
Domain description: RNA polymerase Rpb7-like , N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR045113
Domain description: RNA polymerase subunit Rpb7-like
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR020708
Domain description: DNA-directed RNA polymerase, 14-18kDa subunit, conserved site
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR028363
Domain description: DNA-directed RNA polymerase, subunit RPB6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR020608
Domain description: RNA polymerase, subunit H/Rpb5, conserved site
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR000783
Domain description: RNA polymerase, subunit H/Rpb5 C-terminal
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR005571
Domain description: RNA polymerase, Rpb5, N-terminal
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR038324
Domain description: Rpb4/RPC9 superfamily
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR005574
Domain description: RNA polymerase subunit Rpb4/RPC9
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR010997
Domain description: HRDC-like superfamily
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR006590
Domain description: RNA polymerase Rpb4/RPC9, core
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR045222
Domain description: DNA-directed RNA polymerase II subunit Rpb4-like
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR011262
Domain description: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR001514
Domain description: DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR022842
Domain description: DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR007641
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007121
Domain description: RNA polymerase, beta subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR014724
Domain description: RNA polymerase Rpb2, OB-fold
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR037033
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007120
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007647
Domain description: RNA polymerase Rpb2, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007646
Domain description: RNA polymerase Rpb2, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007645
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR037034
Domain description: RNA polymerase Rpb2, domain 2 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007642
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007644
Domain description: RNA polymerase, beta subunit, protrusion
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR038593
Domain description: RNA polymerase Rpb1, domain 7 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007073
Domain description: RNA polymerase Rpb1, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007075
Domain description: RNA polymerase Rpb1, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007081
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007083
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR038120
Domain description: RNA polymerase Rpb1, funnel domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR042102
Domain description: RNA polymerase Rpb1, domain 3 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007066
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR000722
Domain description: RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR006592
Domain description: RNA polymerase, N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR045867
Domain description: DNA-directed RNA polymerase, subunit beta-prime
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007080
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit

Structure domains

CATH CATH domains
1.10.20.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Histone, subunit A
Homology: Histone, subunit A
Occurring in:
  1. Histone H3.3
  2. Histone H4
  3. Histone H2A type 1-B/E
  4. Histone H2B type 1-J
The deposited structure of PDB entry 6ir9 contains 2 copies of CATH domain 1.10.20.10 (Histone, subunit A) in Histone H3.3. Showing 1 copy in chain S [auth a].
The deposited structure of PDB entry 6ir9 contains 2 copies of CATH domain 1.10.20.10 (Histone, subunit A) in Histone H4. Showing 1 copy in chain T [auth b].
The deposited structure of PDB entry 6ir9 contains 2 copies of CATH domain 1.10.20.10 (Histone, subunit A) in Histone H2A type 1-B/E. Showing 1 copy in chain Y [auth g].
The deposited structure of PDB entry 6ir9 contains 2 copies of CATH domain 1.10.20.10 (Histone, subunit A) in Histone H2B type 1-J. Showing 1 copy in chain V [auth d].
3.30.1360.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Gyrase A; domain 2
Homology: RNA polymerase, RBP11-like subunit
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
  2. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.30.1360.10 (Gyrase A; domain 2) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.30.1360.10 (Gyrase A; domain 2) in DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein. Showing 1 copy in chain K.
2.40.50.140
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: Nucleic acid-binding proteins
Occurring in:
  1. DNA-directed RNA polymerase subunit
  2. DNA-directed RNA polymerases I, II, and III subunit RPABC3
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 2.40.50.140 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 2.40.50.140 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerases I, II, and III subunit RPABC3. Showing 1 copy in chain H.
1.20.1250.40
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Growth Hormone; Chain: A;
Homology: Growth Hormone; Chain: A;
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 1.20.1250.40 (Growth Hormone; Chain: A;) in RNA polymerase Rpb4/RPC9 core domain-containing protein. Showing 1 copy in chain D.
3.30.40.210
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Herpes Virus-1
Homology: Herpes Virus-1
Occurring in:
  1. Transcription elongation factor SPT4
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.30.40.210 (Herpes Virus-1) in Transcription elongation factor SPT4. Showing 1 copy in chain Q [auth V].
2.20.25.190
Class: Mainly Beta
Architecture: Single Sheet
Topology: N-terminal domain of TfIIb
Homology: N-terminal domain of TfIIb
Occurring in:
  1. Transcription elongation factor 1 homolog
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 2.20.25.190 (N-terminal domain of TfIIb) in Transcription elongation factor 1 homolog. Showing 1 copy in chain P [auth M].
2.20.28.30
Class: Mainly Beta
Architecture: Single Sheet
Topology: Rubrerythrin, domain 2
Homology: RNA polymerase ii, chain L
Occurring in:
  1. RNA polymerase subunit ABC10-alpha
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 2.20.28.30 (Rubrerythrin, domain 2) in RNA polymerase subunit ABC10-alpha. Showing 1 copy in chain L.
1.10.10.60
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: Homeodomain-like
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC5
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 1.10.10.60 (Arc Repressor Mutant, subunit A) in RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III. Showing 1 copy in chain J.
3.30.1490.120
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Dna Ligase; domain 1
Homology: RNA polymerase Rpb7-like, N-terminal domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.30.1490.120 (Dna Ligase; domain 1) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.
3.90.940.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Eukaryotic RPB6 RNA polymerase subunit
Homology: Eukaryotic RPB6 RNA polymerase subunit
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.90.940.10 (Eukaryotic RPB6 RNA polymerase subunit) in RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III. Showing 1 copy in chain F.
3.90.940.20
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Eukaryotic RPB6 RNA polymerase subunit
Homology: RPB5-like RNA polymerase subunit
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.90.940.20 (Eukaryotic RPB6 RNA polymerase subunit) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.
3.40.1340.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Homology: RNA polymerase, Rpb5, N-terminal domain
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 3.40.1340.10 (Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.
2.170.120.12
Class: Mainly Beta
Architecture: Beta Complex
Topology: RNA Polymerase Alpha Subunit; Chain A, domain 2
Homology: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
The deposited structure of PDB entry 6ir9 contains 1 copy of CATH domain 2.170.120.12 (RNA Polymerase Alpha Subunit; Chain A, domain 2) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.