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

Source organisms:
Biochemical function: DNA binding
Biological process: DNA-templated transcription
Cellular component: nucleus

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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 8jh2 contains 15 copies of Pfam domain PF05001 (RNA polymerase Rpb1 C-terminal repeat ) in DNA-directed RNA polymerase subunit. Showing 15 copies in chain C [auth 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 8jh2 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H3.3. Showing 1 copy in chain Y [auth e].
The deposited structure of PDB entry 8jh2 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 W [auth c].
The deposited structure of PDB entry 8jh2 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H2B type 1-J. Showing 1 copy in chain BA [auth h].

PF16211
Domain description: C-terminus of histone H2A
Occurring in:
  1. Histone H2A type 1-B/E
The deposited structure of PDB entry 8jh2 contains 2 copies of Pfam domain PF16211 (C-terminus of histone H2A) in Histone H2A type 1-B/E. Showing 1 copy in chain W [auth c].

PF15511
Domain description: Centromere kinetochore component CENP-T histone fold
Occurring in:
  1. Histone H4
The deposited structure of PDB entry 8jh2 contains 2 copies of Pfam domain PF15511 (Centromere kinetochore component CENP-T histone fold) in Histone H4. Showing 1 copy in chain Z [auth f].

PF00467
Domain description: KOW motif
Occurring in:
  1. Transcription elongation factor SPT5
The deposited structure of PDB entry 8jh2 contains 2 copies of Pfam domain PF00467 (KOW motif) in Transcription elongation factor SPT5. Showing 2 copies in chain T [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 8jh2 contains 1 copy of Pfam domain PF12815 (Spt5 C-terminal nonapeptide repeat binding Spt4) in Transcription elongation factor SPT5. Showing 1 copy in chain T [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 8jh2 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 T [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 8jh2 contains 1 copy of Pfam domain PF11942 (Spt5 transcription elongation factor, acidic N-terminal) in Transcription elongation factor SPT5. Showing 1 copy in chain T [auth W].

PF06093
Domain description: Spt4/RpoE2 zinc finger
Occurring in:
  1. Transcription elongation factor SPT4
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF06093 (Spt4/RpoE2 zinc finger) in Transcription elongation factor SPT4. Showing 1 copy in chain S [auth V].

PF05129
Domain description: Transcription elongation factor Elf1 like
Occurring in:
  1. Transcription elongation factor 1 homolog
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF05129 (Transcription elongation factor Elf1 like) in Transcription elongation factor 1 homolog. Showing 1 copy in chain O [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 8jh2 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 N [auth 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 8jh2 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 M [auth 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 8jh2 contains 1 copy of Pfam domain PF01194 (RNA polymerases N / 8 kDa subunit) in DNA-directed RNA polymerases I, II, and III subunit RPABC5. Showing 1 copy in chain L [auth J].

PF01096
Domain description: Transcription factor S-II (TFIIS)
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF01096 (Transcription factor S-II (TFIIS)) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain K [auth I].

PF02150
Domain description: RNA polymerases M/15 Kd subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF02150 (RNA polymerases M/15 Kd subunit) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain K [auth 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 8jh2 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 J [auth H].

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF00575 (S1 RNA binding domain) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain I [auth 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 8jh2 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 I [auth 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 8jh2 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 H [auth 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 8jh2 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 G [auth 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 8jh2 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 G [auth E].

PF03874
Domain description: RNA polymerase Rpb4
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF03874 (RNA polymerase Rpb4) in RNA polymerase Rpb4/RPC9 core domain-containing protein. Showing 1 copy in chain F [auth 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 8jh2 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 E [auth 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 8jh2 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 E [auth C].
The deposited structure of PDB entry 8jh2 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 M [auth K].

PF04560
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04560 (RNA polymerase Rpb2, domain 7) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF00562
Domain description: RNA polymerase Rpb2, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF00562 (RNA polymerase Rpb2, domain 6) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04567
Domain description: RNA polymerase Rpb2, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04567 (RNA polymerase Rpb2, domain 5) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04566
Domain description: RNA polymerase Rpb2, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04566 (RNA polymerase Rpb2, domain 4) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04565
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04565 (RNA polymerase Rpb2, domain 3) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04561
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04561 (RNA polymerase Rpb2, domain 2) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04563
Domain description: RNA polymerase beta subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04563 (RNA polymerase beta subunit) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain D [auth B].

PF04990
Domain description: RNA polymerase Rpb1, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04990 (RNA polymerase Rpb1, domain 7) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF04992
Domain description: RNA polymerase Rpb1, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04992 (RNA polymerase Rpb1, domain 6) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF04998
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04998 (RNA polymerase Rpb1, domain 5) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF05000
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF05000 (RNA polymerase Rpb1, domain 4) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF04983
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04983 (RNA polymerase Rpb1, domain 3) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF00623
Domain description: RNA polymerase Rpb1, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF00623 (RNA polymerase Rpb1, domain 2) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

PF04997
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 8jh2 contains 1 copy of Pfam domain PF04997 (RNA polymerase Rpb1, domain 1) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain C [auth A].

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