4G7H | pdb_00004g7h

Crystal structure of Thermus thermophilus transcription initiation complex

PDB DOI: https://doi.org/10.2210/pdb4G7H/pdb
NAKB: 4G7H

Classification: TRANSCRIPTION, TRANSFERASE/DNA
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-20 Released: 2012-10-31
Deposition Author(s): Zhang, Y., Ebright, R.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.226 (Depositor), 0.227 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of transcription initiation.

Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M.X., Arnold, E., Ebright, R.H.

(2012) Science 338: 1076-1080

PubMed: 23086998 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1227786
Primary Citation Related Structures:
4G7H, 4G7O, 4G7Z

PubMed Abstract:
During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.

Organizational Affiliation

Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

Macromolecule Content

Total Structure Weight: 886.69 kDa
Atom Count: 57,420
Modeled Residue Count: 7,054
Deposited Residue Count: 7,722
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B, I [auth K], J [auth L]	315	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR6 Go to UniProtKB: Q5SHR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHR6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C, K [auth M]	1,119	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE9 Go to UniProtKB: Q8RQE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D, L [auth N]	1,524	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE8 Go to UniProtKB: Q8RQE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E, M [auth O]	99	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE7 Go to UniProtKB: Q8RQE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQE7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor	F, N [auth P]	443	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: rpoD, TTHA0532
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW1 Go to UniProtKB: Q5SKW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKW1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
5'-D(CPCPTGPCPAPTPCPCPGPTPGPAPGPTPCPGPAP*G)-3'	G, O [auth Q]	19	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 7
5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPGPCPAPGP*G)-3'	H, P [auth R]	27	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth N] SDF format, chain Y [auth N] SDF format, chain S [auth D] SDF format, chain R [auth D] MOL2 format, chain Z [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] mmCIF format, chain Z [auth N] mmCIF format, chain Y [auth N] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D]	R [auth D], S [auth D], Y [auth N], Z [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Focus chain S [auth D] Focus chain Y [auth N] Focus chain Z [auth N] Interactions & Density Focus chain R [auth D] Focus chain S [auth D] Focus chain Y [auth N] Focus chain Z [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth K] SDF format, chain W [auth F] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth B] SDF format, chain DA [auth P] SDF format, chain CA [auth N] SDF format, chain BA [auth N] SDF format, chain AA [auth N] MOL2 format, chain X [auth K] MOL2 format, chain W [auth F] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain DA [auth P] MOL2 format, chain CA [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain AA [auth N] mmCIF format, chain X [auth K] mmCIF format, chain W [auth F] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain DA [auth P] mmCIF format, chain CA [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain AA [auth N]	AA [auth N] BA [auth N] CA [auth N] DA [auth P] Q [auth B] AA [auth N], BA [auth N], CA [auth N], DA [auth P], Q [auth B], T [auth D], U [auth D], V [auth D], W [auth F], X [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth N] Focus chain CA [auth N] Focus chain DA [auth P] Focus chain Q [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth F] Focus chain X [auth K] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth N] Focus chain CA [auth N] Focus chain DA [auth P] Focus chain Q [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth F] Focus chain X [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.226 (Depositor), 0.227 (DCC)
R-Value Work: 0.188 (Depositor), 0.195 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.56	α = 90
b = 104.57	β = 98.32
c = 297.55	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-10-31

Deposition Author(s):

Zhang, Y.

Ebright, R.H.

Revision History (Full details and data files)

Version 1.0: 2012-10-31
Type: Initial release
Version 1.1: 2012-11-07
Changes: Database references
Version 1.2: 2012-12-12
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4G7H | pdb_00004g7h

Crystal structure of Thermus thermophilus transcription initiation complex

Literature

Structural basis of transcription initiation.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

Sequence Annotations

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Entity ID: 7

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)