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CryoEM structure of E.coli RNA polymerase paused elongation complex without RNA hairpin bound to NusA

Source organism: Escherichia coli K-12
Biochemical function: 5'-3' RNA polymerase activity
Biological process: regulation of DNA-templated transcription initiation
Cellular component: transcription elongation factor complex

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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

Sequence families

Pfam Protein families (Pfam)
PF00623
Domain description: RNA polymerase Rpb1, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 6flp contains 2 copies of Pfam domain PF00623 (RNA polymerase Rpb1, domain 2) in DNA-directed RNA polymerase subunit beta'. Showing 2 copies in chain D.

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

PF03118
Domain description: Bacterial RNA polymerase, alpha chain C terminal domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 6flp contains 2 copies of Pfam domain PF03118 (Bacterial RNA polymerase, alpha chain C terminal domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain A (this domain is out of the observed residue ranges!).

PF01000
Domain description: RNA polymerase Rpb3/RpoA insert domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 6flp contains 2 copies of Pfam domain PF01000 (RNA polymerase Rpb3/RpoA insert domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain A.

PF01193
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 6flp contains 2 copies of Pfam domain PF01193 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain A.

PF01192
Domain description: RNA polymerase Rpb6
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
The deposited structure of PDB entry 6flp contains 1 copy of Pfam domain PF01192 (RNA polymerase Rpb6) in DNA-directed RNA polymerase subunit omega. Showing 1 copy in chain E.

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

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

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

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

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

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

PF10385
Domain description: RNA polymerase beta subunit external 1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 6flp contains 1 copy of Pfam domain PF10385 (RNA polymerase beta subunit external 1 domain) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain C.

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

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

InterPro InterPro annotations
IPR036643
Domain description: DNA-directed RNA polymerase, insert domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011263
Domain description: DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR036603
Domain description: RNA polymerase, RBP11-like subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011773
Domain description: DNA-directed RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR003716
Domain description: DNA-directed RNA polymerase, omega subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR006110
Domain description: RNA polymerase, subunit omega/Rpo6/RPB6
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR036161
Domain description: RPB6/omega subunit-like superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR000722
Domain description: RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR012754
Domain description: DNA-directed RNA polymerase, subunit beta-prime, bacterial type
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
IPR015712
Domain description: DNA-directed RNA polymerase, subunit 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR010243
Domain description: DNA-directed RNA polymerase beta subunit, bacterial-type
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR011260
Domain description: RNA polymerase, alpha subunit, C-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011262
Domain description: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR007081
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007083
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR038120
Domain description: RNA polymerase Rpb1, funnel domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR042102
Domain description: RNA polymerase Rpb1, domain 3 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007066
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR006592
Domain description: RNA polymerase, N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR045867
Domain description: DNA-directed RNA polymerase, subunit beta-prime
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007080
Domain description: RNA polymerase Rpb1, domain 1
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 beta'
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
IPR037033
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
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
IPR007120
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR019462
Domain description: DNA-directed RNA polymerase, beta subunit, external 1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR042107
Domain description: DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily
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
IPR007644
Domain description: RNA polymerase, beta subunit, protrusion
Occurring in:
  1. DNA-directed RNA polymerase subunit beta

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