8QU6

Mycobacterium smegnatis RNA polymerase transcription initiation complex with SigmaA, RbpA, HelD and an upstream-fork promoter fragment

PDB DOI: https://doi.org/10.2210/pdb8QU6/pdb
EM Map EMD-18656: EMDB EMDataResource
NAKB: 8QU6

Classification: TRANSCRIPTION
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-13 Released: 2024-10-02
Deposition Author(s): Koval, T., Krasny, L., Dohnalek, J., Kouba, T.
Funding Organization(s): Grant Agency of the Czech Republic, Ministry of Education (MoE, Czech Republic), Czech Academy of Sciences, European Union (EU)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Molecular insights into RNA polymerase recycling by mycobacterial HelD

Koval, T., Dohnalek, L., Libor, K., Kouba, T.

To be published.

Macromolecule Content

Total Structure Weight: 525.21 kDa
Atom Count: 32,464
Modelled Residue Count: 4,078
Deposited Residue Count: 4,662
Unique protein chains: 7
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	350	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL8 Go to UniProtKB: A0QSL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSL8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,169	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore P60281 Go to UniProtKB: P60281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60281
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,317	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS66 Go to UniProtKB: A0QS66
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QS66
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-binding protein RbpA	E [auth J]	114	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: rbpA, MSMEG_3858, MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QZ11 Go to UniProtKB: A0QZ11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QZ11
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	F [auth E]	107	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: rpoZ, MSMEG_3053, MSMEI_2977 EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QWT1 Go to UniProtKB: A0QWT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QWT1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA	G [auth F]	466	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: sigA, MSMEG_2758
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QW02 Go to UniProtKB: A0QW02
Entity Groups
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UniProt Group	A0QW02
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	H	736	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEI_2121
UniProt
Find proteins for I7G5V9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7G5V9 Go to UniProtKB: I7G5V9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7G5V9
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA 22-MER	I [auth P]	22	Mycolicibacterium smegmatis MC2 155
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Length	Organism	Image
DNA 31-MER	J [auth O]	31	Mycolicibacterium smegmatis MC2 155
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 K [auth D] SDF format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain K [auth D] Focus chain L [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	23-06295S
Ministry of Education (MoE, Czech Republic)	Czech Republic	LM2023042
Czech Academy of Sciences	Czech Republic	86652036
Grant Agency of the Czech Republic	Czech Republic	23-06295S
European Union (EU)	European Union	LX22NPO5103