7Q4U | pdb_00007q4u

Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase holoenzyme octamer comprising sigma factor SigB

PDB DOI: https://doi.org/10.2210/pdb7Q4U/pdb
EM Map EMD-13817: EMDB EMDataResource

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

Deposited: 2021-11-02 Released: 2022-11-16
Deposition Author(s): Brodolin, K.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization

Morichaud, Z., Trapani, S., Vishwakarma, R.K., Chaloin, L., Lionne, C., Lai-Kee-Him, J., Bron, P., Brodolin, K.

(2023) Nat Commun 14: 484

DOI: https://doi.org/10.1038/s41467-023-36113-y

Macromolecule Content

Total Structure Weight: 3,224.88 kDa
Atom Count: 190,528
Modeled Residue Count: 24,472
Deposited Residue Count: 29,120
Unique protein chains: 5

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 EA [auth FA] FA [auth GA] G A, B, EA [auth FA], FA [auth GA], G, H, KA [auth LA], LA [auth MA], M, N, QA [auth RA], RA [auth SA], S, T, Y [auth Z], Z [auth AA]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGZ1
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	AA [auth BA] C GA [auth HA] I MA [auth NA] AA [auth BA], C, GA [auth HA], I, MA [auth NA], O, SA [auth TA], U [auth V]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY9
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'	BA [auth CA] D HA [auth IA] J NA [auth OA] BA [auth CA], D, HA [auth IA], J, NA [auth OA], P, TA [auth UA], V [auth W]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY7
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	CA [auth DA] E IA [auth JA] K OA [auth PA] CA [auth DA], E, IA [auth JA], K, OA [auth PA], Q, UA [auth VA], W [auth X]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGY5
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 SigB	DA [auth EA] F JA [auth KA] L PA [auth QA] DA [auth EA], F, JA [auth KA], L, PA [auth QA], R, VA [auth WA], X [auth Y]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth J] SDF format, chain XA [auth D] SDF format, chain WA [auth D] SDF format, chain SB [auth UA] SDF format, chain RB [auth UA] SDF format, chain PB [auth OA] SDF format, chain OB [auth OA] SDF format, chain MB [auth IA] SDF format, chain LB [auth IA] SDF format, chain JB [auth CA] SDF format, chain IB [auth CA] SDF format, chain GB [auth W] SDF format, chain FB [auth W] SDF format, chain DB [auth P] SDF format, chain CB [auth P] SDF format, chain AB [auth J] MOL2 format, chain ZA [auth J] MOL2 format, chain XA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain SB [auth UA] MOL2 format, chain RB [auth UA] MOL2 format, chain PB [auth OA] MOL2 format, chain OB [auth OA] MOL2 format, chain MB [auth IA] MOL2 format, chain LB [auth IA] MOL2 format, chain JB [auth CA] MOL2 format, chain IB [auth CA] MOL2 format, chain GB [auth W] MOL2 format, chain FB [auth W] MOL2 format, chain DB [auth P] MOL2 format, chain CB [auth P] MOL2 format, chain AB [auth J] mmCIF format, chain ZA [auth J] mmCIF format, chain XA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain SB [auth UA] mmCIF format, chain RB [auth UA] mmCIF format, chain PB [auth OA] mmCIF format, chain OB [auth OA] mmCIF format, chain MB [auth IA] mmCIF format, chain LB [auth IA] mmCIF format, chain JB [auth CA] mmCIF format, chain IB [auth CA] mmCIF format, chain GB [auth W] mmCIF format, chain FB [auth W] mmCIF format, chain DB [auth P] mmCIF format, chain CB [auth P] mmCIF format, chain AB [auth J]	AB [auth J] CB [auth P] DB [auth P] FB [auth W] GB [auth W] AB [auth J], CB [auth P], DB [auth P], FB [auth W], GB [auth W], IB [auth CA], JB [auth CA], LB [auth IA], MB [auth IA], OB [auth OA], PB [auth OA], RB [auth UA], SB [auth UA], WA [auth D], XA [auth D], ZA [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain CB [auth P] Focus chain DB [auth P] Focus chain FB [auth W] Focus chain GB [auth W] Focus chain IB [auth CA] Focus chain JB [auth CA] Focus chain LB [auth IA] Focus chain MB [auth IA] Focus chain OB [auth OA] Focus chain PB [auth OA] Focus chain RB [auth UA] Focus chain SB [auth UA] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain CB [auth P] Focus chain DB [auth P] Focus chain FB [auth W] Focus chain GB [auth W] Focus chain IB [auth CA] Focus chain JB [auth CA] Focus chain LB [auth IA] Focus chain MB [auth IA] Focus chain OB [auth OA] Focus chain PB [auth OA] Focus chain RB [auth UA] Focus chain SB [auth UA] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth J]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain TB [auth UA] SDF format, chain QB [auth OA] SDF format, chain NB [auth IA] SDF format, chain KB [auth CA] SDF format, chain HB [auth W] SDF format, chain EB [auth P] SDF format, chain BB [auth J] MOL2 format, chain YA [auth D] MOL2 format, chain TB [auth UA] MOL2 format, chain QB [auth OA] MOL2 format, chain NB [auth IA] MOL2 format, chain KB [auth CA] MOL2 format, chain HB [auth W] MOL2 format, chain EB [auth P] MOL2 format, chain BB [auth J] mmCIF format, chain YA [auth D] mmCIF format, chain TB [auth UA] mmCIF format, chain QB [auth OA] mmCIF format, chain NB [auth IA] mmCIF format, chain KB [auth CA] mmCIF format, chain HB [auth W] mmCIF format, chain EB [auth P] mmCIF format, chain BB [auth J]	BB [auth J] EB [auth P] HB [auth W] KB [auth CA] NB [auth IA] BB [auth J], EB [auth P], HB [auth W], KB [auth CA], NB [auth IA], QB [auth OA], TB [auth UA], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Focus chain EB [auth P] Focus chain HB [auth W] Focus chain KB [auth CA] Focus chain NB [auth IA] Focus chain QB [auth OA] Focus chain TB [auth UA] Focus chain YA [auth D] Interactions & Density Focus chain BB [auth J] Focus chain EB [auth P] Focus chain HB [auth W] Focus chain KB [auth CA] Focus chain NB [auth IA] Focus chain QB [auth OA] Focus chain TB [auth UA] Focus chain YA [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Brodolin, K.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE11-0025

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2023-02-08
Changes: Database references, Refinement description
Version 1.2: 2024-07-17
Changes: Data collection, Refinement description