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- EMDB-62387: The map of StnY-DNA complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62387
TitleThe map of StnY-DNA complex
Map data
Sample
  • Complex: StnY-DNA complex
    • Protein or peptide: StnY-DNA complex
KeywordsInhibitor / DNA BINDING PROTEIN
Biological speciesStreptomyces albus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsYang X / Yang SQ / Zheng JT / Lin SJ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA0914200 China
CitationJournal: To Be Published
Title: RHH family transcription factor serves as molecular switch of antibiotics resistance operon coupling of drug efflux pump and drug binding protein
Authors: Yang SQ / Yang X / Zheng JT / Lin SJ
History
DepositionNov 13, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62387.png

Downloads & links

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Map

FileDownload / File: emd_62387.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.07768724 - 0.2031347
Average (Standard dev.)0.0001615449 (±0.008508397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62387_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62387_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62387_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : StnY-DNA complex

EntireName: StnY-DNA complex
Components
  • Complex: StnY-DNA complex
    • Protein or peptide: StnY-DNA complex

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Supramolecule #1: StnY-DNA complex

SupramoleculeName: StnY-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces albus (bacteria)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: StnY-DNA complex

MacromoleculeName: StnY-DNA complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces albus (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MRQFNVYLPG DLIRQVKHFA IDRELSLSAL VAEALRSYLD EHQRQERDKS IQLEHHHHHH

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
10.0 mMTrisTris

Details: 10 mM Tris, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104773
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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