7VO0

Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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: 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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative metal uptake regulation protein159Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO2508
UniProt
Find proteins for Q9L2H5 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L2H5 
Go to UniProtKB:  Q9L2H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L2H5
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA_NT (84-MER)A84Streptomyces coelicolor A3(2)
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA_T (84-MER)B84Streptomyces coelicolor A3(2)
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
I [auth G],
J [auth G],
K [auth G],
L [auth H],
M [auth H],
I [auth G],
J [auth G],
K [auth G],
L [auth H],
M [auth H],
N [auth H],
O [auth K],
P [auth K],
Q [auth K],
R [auth L],
S [auth L],
T [auth L],
U [auth M],
V [auth M],
W [auth M],
X [auth N],
Y [auth N],
Z [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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)31770068, 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