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- EMDB-32049: Streptomyces coelicolor zinc uptake regulator complexed with zinc... -

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Basic information

Entry
Database: EMDB / ID: EMD-32049
TitleStreptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers)
Map data
Sample
  • Complex: Zur-DNA
    • DNA: DNA (84-MER)
    • DNA: DNA (84-MER)
    • Protein or peptide: Putative metal uptake regulation protein
  • Ligand: ZINC ION
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


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
Zinc uptake regulation protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria) / Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang X / Zheng J
Funding support China, 1 items
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, 2021-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32049.png

Downloads & links

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Map

FileDownload / File: emd_32049.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-3.823014 - 5.9052444
Average (Standard dev.)0.0015566567 (±0.043087214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32049_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_32049_half_map_1.map
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Half map: #1

Fileemd_32049_half_map_2.map
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Sample components

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Entire : Zur-DNA

EntireName: Zur-DNA
Components
  • Complex: Zur-DNA
    • DNA: DNA (84-MER)
    • DNA: DNA (84-MER)
    • Protein or peptide: Putative metal uptake regulation protein
  • Ligand: ZINC ION

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Supramolecule #1: Zur-DNA

SupramoleculeName: Zur-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 250 kDa/nm

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Macromolecule #1: DNA (84-MER)

MacromoleculeName: DNA (84-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 25.808424 KDa
SequenceString: (DC)(DA)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DT) (DG)(DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT)(DG) (DT)(DT)(DC)(DA)(DG)(DT)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DG)(DC)(DC)(DC)(DG) (DA) (DT)(DA)(DC)(DC)(DC)(DC) ...String:
(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DT) (DG)(DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT)(DG) (DT)(DT)(DC)(DA)(DG)(DT)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DG)(DC)(DC)(DC)(DG) (DA) (DT)(DA)(DC)(DC)(DC)(DC)(DC)(DT) (DA)(DC)(DC)(DC)(DG)(DT)(DA)(DG)(DT)(DT) (DG)(DA) (DC)(DT)(DG)(DG)(DC)(DA)(DT) (DC)(DC)(DG)(DG)(DG)(DC)(DG)(DC)(DC)(DG) (DG)(DG)(DT) (DC)(DG)(DC)(DC)

GENBANK: GENBANK: AL939129.1

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Macromolecule #2: DNA (84-MER)

MacromoleculeName: DNA (84-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 26.008541 KDa
SequenceString: (DG)(DG)(DC)(DG)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DG)(DC)(DC)(DG)(DC)(DC)(DT)(DA)(DC) (DG)(DG)(DT)(DC)(DA)(DG)(DT)(DA)(DC) (DT)(DA)(DC)(DG)(DG)(DG)(DT)(DA)(DG)(DG) (DG) (DG)(DG)(DT)(DA)(DT)(DC) ...String:
(DG)(DG)(DC)(DG)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DG)(DC)(DC)(DG)(DC)(DC)(DT)(DA)(DC) (DG)(DG)(DT)(DC)(DA)(DG)(DT)(DA)(DC) (DT)(DA)(DC)(DG)(DG)(DG)(DT)(DA)(DG)(DG) (DG) (DG)(DG)(DT)(DA)(DT)(DC)(DG)(DG) (DG)(DC)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DC) (DA)(DC) (DT)(DG)(DA)(DA)(DC)(DA)(DC) (DC)(DG)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG) (DT)(DG)(DC) (DC)(DT)(DT)(DG)

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Macromolecule #3: Putative metal uptake regulation protein

MacromoleculeName: Putative metal uptake regulation protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145
Molecular weightTheoretical: 16.90484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MTTAGPPVKG RATRQRAAVS AALQEVEEFR SAQELHDMLK HKGDAVGLTT VYRTLQSLAD AGEVDVLRT AEGESVYRRC STGDHHHHLV CRACGKAVEV EGPAVEKWAE AIAAEHGYVN VAHTVEIFGT CADCAGASGG

UniProtKB: Zinc uptake regulation protein

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
20.0 mMHEPES
100.0 mMKCl
2.0 mMDTT
5.0 mMMgCl2
20.0 ?MZnSO4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71726
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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