2a6e Summary

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Crystal structure of the T. Thermophilus RNA polymerase holoenzyme

The structure was published by Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., et al., Wakatsuki, S., Tahirov, T.H., and Vassylyev, D.G., in 2005 in a paper entitled "Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.8 Å and deposited in 2005.

The experimental data on which the structure is based was also deposited.

This entry contains 30 copies of 5 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A DNA-directed RNA polymerase alpha chain Q5SHR6 (1-315) (RPOA_THET8)search Thermus thermophilus HB8search 97% 315 72%
B DNA-directed RNA polymerase alpha chain Q5SHR6 (1-315) (RPOA_THET8)search Thermus thermophilus HB8search 97% 315 72%
K DNA-directed RNA polymerase alpha chain Q5SHR6 (1-315) (RPOA_THET8)search Thermus thermophilus HB8search 97% 315 72%
L DNA-directed RNA polymerase alpha chain Q5SHR6 (1-315) (RPOA_THET8)search Thermus thermophilus HB8search 97% 315 72%
C DNA-directed RNA polymerase beta chain Q8RQE9 (1-1119) (RPOB_THET8)search Thermus thermophilus HB8search 100% 1119 100%
M DNA-directed RNA polymerase beta chain Q8RQE9 (1-1119) (RPOB_THET8)search Thermus thermophilus HB8search 100% 1119 100%
D DNA-directed RNA polymerase beta' chain Q8RQE8 (1-1524) (RPOC_THET8)search Thermus thermophilus HB8search 100% 1524 91%
N DNA-directed RNA polymerase beta' chain Q8RQE8 (1-1524) (RPOC_THET8)search Thermus thermophilus HB8search 100% 1524 91%
E RNA polymerase omega chain Q8RQE7 (1-99) (RPOZ_THET8)search Thermus thermophilus HB8search 100% 99 95%
O RNA polymerase omega chain Q8RQE7 (1-99) (RPOZ_THET8)search Thermus thermophilus HB8search 100% 99 95%
F RNA polymerase sigma factor rpoD Q5SKW1 (1-423) (Q5SKW1_THET8)search Thermus thermophilus HB8search 100% 423 81%
P RNA polymerase sigma factor rpoD Q5SKW1 (1-423) (Q5SKW1_THET8)search Thermus thermophilus HB8search 100% 423 81%


This entry contains 5 unique UniProt proteins:

UniProt accession Name Organism PDB
Q5SHR6 (1 - 315) DNA-directed RNA polymerase alpha chain Thermus thermophilus
Q8RQE9 (1 - 1119) DNA-directed RNA polymerase beta chain Thermus thermophilus
Q8RQE8 (1 - 1524) DNA-directed RNA polymerase beta' chain Thermus thermophilus
Q8RQE7 (1 - 99) RNA polymerase omega chain Thermus thermophilus
Q5SKW1 (1 - 423) RNA polymerase sigma factor rpoD Thermus thermophilus

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, B, K, L (Q5SHR6) RNA polymerase alpha subunit dimerisation domainsearch, Insert subdomain of RNA polymerase alpha subunitsearch Gyrase A; domain 2search, RNA Polymerase Alpha Subunit; Chain A, domain 2search PF01193: RNA polymerase Rpb3/Rpb11 dimerisation domainsearch, PF03118: Bacterial RNA polymerase, alpha chain C terminal domainsearch
C, M (Q8RQE9) RNA-polymerase betasearch Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6search, Rna Polymerase Beta Subunit; Chain: C,domain 2search, Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3search, Rna Polymerase Beta Subunit; Chain: C, domain 4search, OB fold (Dihydrolipoamide Acetyltransferase, E2P)search PF00562: RNA polymerase Rpb2, domain 6search, PF04560: RNA polymerase Rpb2, domain 7search, PF04563: RNA polymerase beta subunitsearch, PF04565: RNA polymerase Rpb2, domain 3search, PF10385: RNA polymerase beta subunit external 1 domainsearch
D, N (Q8RQE8) RNA-polymerase beta-primesearch PF00623: RNA polymerase Rpb1, domain 2search, PF04983: RNA polymerase Rpb1, domain 3search, PF04997: RNA polymerase Rpb1, domain 1search, PF04998: RNA polymerase Rpb1, domain 5search, PF05000: RNA polymerase Rpb1, domain 4search
E, O (Q8RQE7) RNA polymerase omega subunitsearch Eukaryotic RPB6 RNA polymerase subunitsearch PF01192: RNA polymerase Rpb6search
F, P (Q5SKW1) Sigma3 domainsearch, Sigma4 domainsearch, Sigma2 domain of RNA polymerase sigma factorssearch "winged helix" repressor DNA binding domainsearch PF00140: Sigma-70 factor, region 1.2search, PF04539: Sigma-70 region 3search, PF04542: Sigma-70 region 2search, PF04545: Sigma-70, region 4search

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A, B, K, L (Q5SHR6) transcription, DNA-templatedsearch DNA-directed RNA polymerase activitysearch DNA bindingsearch nucleotidyltransferase activitysearch protein dimerization activitysearch transferase activitysearch
C, M (Q8RQE9) transcription, DNA-templatedsearch DNA-directed RNA polymerase activitysearch DNA bindingsearch nucleotidyltransferase activitysearch transferase activitysearch ribonucleoside bindingsearch
D, N (Q8RQE8) transcription, DNA-templatedsearch DNA-directed RNA polymerase activitysearch DNA bindingsearch transferase activitysearch nucleotidyltransferase activitysearch
E, O (Q8RQE7) transcription, DNA-templatedsearch DNA bindingsearch nucleotidyltransferase activitysearch DNA-directed RNA polymerase activitysearch transferase activitysearch
F, P (Q5SKW1) regulation of transcription, DNA-templatedsearch DNA-templated transcription, initiationsearch regulation of gene expressionsearch transcription initiation from bacterial-type RNA polymerase promotersearch transcription, DNA-templatedsearch sequence-specific DNA binding transcription factor activitysearch sigma factor activitysearch DNA bindingsearch metal ion bindingsearch cytoplasmsearch

Chain InterPro annotation
A, B, K, L Helix-hairpin-helix DNA-binding motif, class 1search DNA-directed RNA polymerase, RBP11-like dimerisation domainsearch RNA polymerase, alpha subunit, C-terminalsearch DNA-directed RNA polymerase, insert domainsearch DNA-directed RNA polymerase, RpoA/D/Rpb3-typesearch DNA-directed RNA polymerase, alpha subunitsearch
C, M DNA-directed RNA polymerase, subunit 2, domain 6search RNA polymerase, beta subunit, conserved sitesearch RNA polymerase Rpb2, domain 7search RNA polymerase Rpb2, domain 2search RNA polymerase, beta subunit, protrusionsearch RNA polymerase Rpb2, domain 3search DNA-directed RNA polymerase, beta subunitsearch RNA polymerase Rpb2, OB-foldsearch DNA-directed RNA polymerase, subunit 2search DNA-directed RNA polymerase, beta subunit, external 1 domainsearch
D, N RNA polymerase, alpha subunitsearch RNA polymerase, N-terminalsearch RNA polymerase Rpb1, domain 3search RNA polymerase Rpb1, domain 1search RNA polymerase Rpb1, domain 5search RNA polymerase Rpb1, domain 4search DNA-directed RNA polymerase, subunit beta-primesearch
E, O DNA-directed RNA polymerase, omega subunitsearch RNA polymerase, subunit omega/K/RPB6search RNA polymerase subunit, RPB6/omegasearch
F, P RNA polymerase sigma-70search RNA polymerase sigma-70 region 3search RNA polymerase sigma-70 region 2search RNA polymerase sigma-70 region 4search RNA polymerase sigma-70 region 1.2search Winged helix-turn-helix DNA-binding domainsearch RNA polymerase sigma factor RpoD, C-terminalsearch RNA polymerase sigma factor, region 3/4search RNA polymerase sigma factor, region 2search RNA polymerase sigma-70 like domainsearch RNA polymerase sigma factor RpoDsearch