6N4C | pdb_00006n4c

EM structure of the DNA wrapping in bacterial open transcription initiation complex

PDB DOI: https://doi.org/10.2210/pdb6N4C/pdb
EM Map EMD-0340: EMDB EMDataResource
NAKB: 6N4C

Classification: transcription/dna
Organism(s): Escherichia coli K-12, Lambdavirus lambda
Mutation(s): No

Deposited: 2018-11-19 Released: 2020-05-27
Deposition Author(s): Florez-Ariza, A., Cassago, A., de Oliveira, P.S.L., Guerra, D.G., Portugal, R.V.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 17.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation

Sosa, R., Florez-Ariza, A., Diaz-Celis, C., Onoa, B., Cassago, A., de Oliveira, P.S.L., Portugal, R.V., Guerra, D.G., Bustamante, C.

(2020) bioRxiv

DOI: https://doi.org/10.1101/2020.05.13.070375

Macromolecule Content

Total Structure Weight: 503.11 kDa
Atom Count: 35,052
Modeled Residue Count: 4,161
Deposited Residue Count: 4,161
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoD	A [auth F]	558	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P00579 (Escherichia coli (strain K12)) Explore P00579 Go to UniProtKB: P00579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00579
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	B [auth C]	1,341	Escherichia coli K-12	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2 Go to UniProtKB: P0A8V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8V2
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'	C [auth D]	1,358	Escherichia coli K-12	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7 Go to UniProtKB: P0A8T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8T7
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 alpha	D [auth A]	316	Escherichia coli K-12	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	E [auth B]	310	Escherichia coli K-12	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	F [auth E]	90	Escherichia coli K-12	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800 Go to UniProtKB: P0A800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A800
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 7
DNA (94-MER)	G [auth a]	94	Lambdavirus lambda
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
DNA (94-MER)	H [auth b]	94	Lambdavirus lambda
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 17.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	IMAGIC

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Refinement description, Structure summary