9FJP | pdb_00009fjp

Cryo-EM structure of Mycobacterium tuberculosis sigma-B RNA polymerase bound to -10 promoter element ssDNA oligo

PDB DOI: https://doi.org/10.2210/pdb9FJP/pdb
EM Map EMD-50508: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Mycobacterium tuberculosis H37Rv, Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-31 Released: 2025-04-02
Deposition Author(s): Brodolin, K., Marechal, N.
Funding Organization(s): Agence Nationale de la Recherche (ANR), Instruct-ERIC Center (Strasbourg Centre)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Single-stranded DNA drives sigma subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations

Vishwakarma, R.K., Marechal, N., Morichaud, Z., Makrini, L., Blaise, M., Margeat, E., Brodolin, K.

(2025) Nucleic Acids Res

DOI: https://doi.org/10.1093/nar/gkaf272

Macromolecule Content

Total Structure Weight: 408.1 kDa
Atom Count: 25,376
Modelled Residue Count: 3,238
Deposited Residue Count: 3,656
Unique protein chains: 5
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A [auth a], B [auth b]	347	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rpoA, Rv3457c, MTCY13E12.10c EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ1 Go to UniProtKB: P9WGZ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGZ1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C [auth c]	1,174	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rpoB, Rv0667, MTCI376.08c EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY9 Go to UniProtKB: P9WGY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGY9
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D [auth d]	1,319	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rpoC, Rv0668, MTCI376.07c EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY7 Go to UniProtKB: P9WGY7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGY7
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E [auth e]	110	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rpoZ, Rv1390, MTCY21B4.07 EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY5 Go to UniProtKB: P9WGY5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGY5
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigB	F [auth f]	343	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: sigB, mysB, Rv2710
UniProt
Find proteins for P9WGI5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGI5 Go to UniProtKB: P9WGI5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGI5
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (17-MER)	G [auth O]	16	Escherichia coli
Sequence Annotations Expand
Reference Sequence LOADING

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 H [auth d] SDF format, chain I [auth d] MOL2 format, chain H [auth d] MOL2 format, chain I [auth d] mmCIF format, chain H [auth d] mmCIF format, chain I [auth d]	H [auth d], I [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth d] Focus chain I [auth d] Interactions & Density Focus chain H [auth d] Focus chain I [auth d]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth d] MOL2 format, chain J [auth d] mmCIF format, chain J [auth d]	J [auth d]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth d] Interactions & Density Focus chain J [auth d]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Brodolin, K.

Marechal, N.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE44-0020-01
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE11-0025
Instruct-ERIC Center (Strasbourg Centre)	France	19348