6Z11 | pdb_00006z11

Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State III, primary channel dis-engaged and active site interfering

• PDB DOI: https://doi.org/10.2210/pdb6Z11/pdb
• EM Map EMD-11026: EMDB EMDataResource

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


• Deposited: 2020-05-11 Released: 2020-11-04 
• Deposition Author(s): Kouba, T., Koval, T., Krasny, L., Dohnalek, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

HelD, a helicase-like protein from gram-positive bacteria in complex with RNA polymerase

Kouba, T., Koval, T., Dohnalek, J., Krasny, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 444.31 kDa 
• Atom Count: 23,948 
• Modeled Residue Count: 3,077 
• Deposited Residue Count: 4,029 
• Unique protein chains: 5

Macromolecules

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  Gene Names: rpoA, MSMEG_1524, MSMEI_1488 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 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  Gene Names: rpoB, MSMEG_1367, MSMEI_1328 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 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  Gene Names: rpoC, MSMEG_1368, MSMEI_1329 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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-associated transcription factor HelD	F [auth H]	736	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_2174 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt), 3.6.5 (UniProt)
UniProt
Find proteins for A0QUE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QUE0  Go to UniProtKB:  A0QUE0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth D], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Kouba, T., Koval, T., Krasny, L., Dohnalek, J.

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection, Database references, Refinement description