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Yorodumi- EMDB-32049: Streptomyces coelicolor zinc uptake regulator complexed with zinc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32049 | |||||||||
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Title | Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA 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 | |||||||||
Biological species | Streptomyces coelicolor A3(2) (bacteria) / Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Yang X / Zheng J | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32049.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-32049-v30.xml emd-32049.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
Images | emd_32049.png | 62.2 KB | ||
Masks | emd_32049_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-32049.cif.gz | 5.7 KB | ||
Others | emd_32049_half_map_1.map.gz emd_32049_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32049 | HTTPS FTP |
-Validation report
Summary document | emd_32049_validation.pdf.gz | 615.3 KB | Display | EMDB validaton report |
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Full document | emd_32049_full_validation.pdf.gz | 614.9 KB | Display | |
Data in XML | emd_32049_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_32049_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32049 | HTTPS FTP |
-Related structure data
Related structure data | 7vo9MC 7vo0C 7vpdC 7vpzC 7x74C 7x75C 7x76C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32049.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_32049_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_32049_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32049_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zur-DNA
Entire | Name: Zur-DNA |
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Components |
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-Supramolecule #1: Zur-DNA
Supramolecule | Name: Zur-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) |
Molecular weight | Theoretical: 250 kDa/nm |
-Macromolecule #1: DNA (84-MER)
Macromolecule | Name: DNA (84-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) |
Molecular weight | Theoretical: 25.808424 KDa |
Sequence | 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) ...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 |
-Macromolecule #2: DNA (84-MER)
Macromolecule | Name: DNA (84-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) |
Molecular weight | Theoretical: 26.008541 KDa |
Sequence | 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) ...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) |
-Macromolecule #3: Putative metal uptake regulation protein
Macromolecule | Name: Putative metal uptake regulation protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 |
Molecular weight | Theoretical: 16.90484 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MTTAGPPVKG RATRQRAAVS AALQEVEEFR SAQELHDMLK HKGDAVGLTT VYRTLQSLAD AGEVDVLRT AEGESVYRRC STGDHHHHLV CRACGKAVEV EGPAVEKWAE AIAAEHGYVN VAHTVEIFGT CADCAGASGG UniProtKB: Metal uptake regulation protein |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |