7VPD

Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with one Zur dimers

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


Literature

Structural basis of Streptomyces transcription activation by zinc uptake regulator.

Yang, X., Wang, Y., Liu, G., Deng, Z., Lin, S., Zheng, J.

(2022) Nucleic Acids Res 50: 8363-8376

  • DOI: https://doi.org/10.1093/nar/gkac627
  • Primary Citation of Related Structures:  
    7VO0, 7VO9, 7VPD, 7VPZ, 7X74, 7X75, 7X76

  • PubMed Abstract: 

    • Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of -35 elements ...

    Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of -35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with promoter DNA and Sc RNA polymerase (RNAP) by cryo-EM structures and biochemical assays. The ScZur-DNA structures reveal a sequential and cooperative binding of three ScZur dimers surrounding a Zur-box spaced 8 nt upstream from a -35 element. The ScRNAPσHrdB-Zur-DNA structures define protein-protein and protein-DNA interactions involved in the principal housekeeping σHrdB-dependent transcription initiation from a noncanonical promoter with a -10 element lacking the critical adenine residue at position -11 and a TTGCCC -35 element deviating from the canonical TTGACA motif. ScZur interacts with the C-terminal domain of ScRNAP α subunit (αCTD) in a complex structure trapped in an active conformation. Key ScZur-αCTD interfacial residues accounting for ScZur-dependent transcription activation were confirmed by mutational studies. Together, our structural and biochemical results provide a comprehensive model for transcription activation of Zur family regulators.

    Organizational Affiliation: 

    Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA,
B,
K [auth S]		340Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: rpoA, GTW64_13255
EC: 2.7.7.6
UniProt
Find proteins for A0A6G2M9E1 (Streptomyces sp. SID4923)
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UniProt GroupA0A6G2M9E1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,161Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: rpoB, SCO4654, SCD82.26
EC: 2.7.7.6
UniProt
Find proteins for Q9L0L0 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,307Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: rpoC, SCO4655, SCD40A.01, SCD82.27
EC: 2.7.7.6
UniProt
Find proteins for Q8CJT1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega90Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: rpoZ, SCO1478, SC9C5.02c
EC: 2.7.7.6
UniProt
Find proteins for Q9KXS1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA532Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: sigA, SLI_6088
UniProt
Find proteins for A0A7U9DYK1 (Streptomyces lividans 1326)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Putative metal uptake regulation proteinG [auth M],
H [auth N]		159Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO2508
UniProt
Find proteins for Q9L2H5 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (84-MER)I [auth O]84Streptomyces coelicolor A3(2)
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (84-MER)J [auth P]84Streptomyces coelicolor A3(2)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770068, 32070040

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references