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- PDB-7vo9: Streptomyces coelicolor zinc uptake regulator complexed with zinc... -

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Basic information

Entry
Database: PDB / ID: 7vo9
TitleStreptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers)
Components
  • (DNA (84-MER)) x 2
  • Putative metal uptake regulation protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Metal uptake regulation protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
Streptomyces coelicolor A3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang, X. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068, 32070040 China
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Authors: Xu Yang / Yiqun Wang / Guiyang Liu / Zixin Deng / Shuangjun Lin / Jianting Zheng /
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 ...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.
History
DepositionOct 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (84-MER)
B: DNA (84-MER)
G: Putative metal uptake regulation protein
H: Putative metal uptake regulation protein
M: Putative metal uptake regulation protein
N: Putative metal uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,22118
Polymers119,4366
Non-polymers78512
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (84-MER)


Mass: 25808.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria) / References: GenBank: 24418971
#2: DNA chain DNA (84-MER)


Mass: 26008.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)
#3: Protein
Putative metal uptake regulation protein


Mass: 16904.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO2508 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L2H5
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Zur-DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 250 kDa/nm / Experimental value: YES
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2100 mMKCl1
32 mMDTT1
45 mMMgCl21
520 ?MZnSO41
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging
IDAccelerating voltage (kV)Electron sourceIllumination modeModelModeSpecimen-ID
1300FIELD EMISSION GUNFLOOD BEAMFEI TITAN KRIOSBRIGHT FIELDBright-field microscopy1
2300FIELD EMISSION GUNFLOOD BEAMFEI TITAN KRIOSBRIGHT FIELDBright-field microscopy1
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
111.25GATAN K2 QUANTUM (4k x 4k)
221.25GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71726 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065964
ELECTRON MICROSCOPYf_angle_d0.698449
ELECTRON MICROSCOPYf_dihedral_angle_d27.3841422
ELECTRON MICROSCOPYf_chiral_restr0.042956
ELECTRON MICROSCOPYf_plane_restr0.005802

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