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- EMDB-56257: CryoEM structure of DruH from Druantia type III -

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Basic information

Entry
Database: EMDB / ID: EMD-56257
TitleCryoEM structure of DruH from Druantia type III
Map data
Sample
  • Complex: DruH
    • Protein or peptide: DruH
Keywordsimmunity / Druantia type III / immunoglobulin / unknown function
Function / homology:
Function and homology information
Biological speciesEscherichia coli O157:H7 str. EDL933 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGrass LM / Himpich S / Hilal T / Loll B / Wahl MC
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2473-2/C4 392923329 Germany
CitationJournal: To Be Published
Title: CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - monomer
Authors: Grass LM / Himpich S / Hilal T / Loll B / Wahl MC
History
DepositionJan 8, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56257.png

Downloads & links

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Map

FileDownload / File: emd_56257.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 252.288 Å		0.66 Å/pix.
x 384 pix.
= 252.288 Å		0.66 Å/pix.
x 384 pix.
= 252.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.0 - 1.7824601
Average (Standard dev.)0.005045525 (±0.033490647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 252.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56257_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 : DruH

EntireName: DruH
Components
  • Complex: DruH
    • Protein or peptide: DruH

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Supramolecule #1: DruH

SupramoleculeName: DruH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)

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Macromolecule #1: DruH

MacromoleculeName: DruH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)
Molecular weightTheoretical: 127.79568 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMETPVNPL LQWLNMFFSR RSLSGADGRA LYAYRCTDTE YESLAELLRT YAPRSYPRTI FISYSDVLFS IYAAEFIRRT HTVGHPKWD TILDSINWKV PYVHRQKLVN DGIRYWKRKI RNLGQASGYL HTLACEGGLP IRMIENESGY LITYFRRIYQ A LRGQSSQY ...String:
GAMETPVNPL LQWLNMFFSR RSLSGADGRA LYAYRCTDTE YESLAELLRT YAPRSYPRTI FISYSDVLFS IYAAEFIRRT HTVGHPKWD TILDSINWKV PYVHRQKLVN DGIRYWKRKI RNLGQASGYL HTLACEGGLP IRMIENESGY LITYFRRIYQ A LRGQSSQY PAAKIAQELG DTIPVTMQNE LVYEIAGEFC ETLCRLLSEH PPHSSDPVSA LRKLSPDWHL QLPLVLPEAN AA EIVRRLL SQSSEIRSAS SLQVERIWVD VDDSWYCDAR FRFPATMRTE QLTSLFECHI QPEQTRLIIS GKWKNGGARL AML SRYEQQ DWRVELLPIA MQKLSGADAM AEISLSLHEG PILLGHTIPK GGYELTEELP WVFEAMNESE SQLKLVGMGS VSSR LNALF ISLPKNSHLD ISGEGEFDIP RLLKNSERSL TKISGVFSVV LHDGAVCTIR TQQLYDSAIE YYIKSTEVEL VKSDY PVHR AWPKIGWKKD LQYGIVPEKE LFWRSIRSGN NAWYSVASEM PKGQIEVRRI VNDEVLFSGK VVVLPADFDI NIIPES AQQ GIIMLSGITD TRIDKYSNNE KVTLKSDYSQ NECAIYYNSS LMLENTVDLR VSWKDGSNLK LLLPKPVSGG RFVTNDG SV HFDGVASIAH LHGIDAELLT ISCAGRGYLN IELLDENPVA EKFRYLHADL PLLSGRNDKL QQISLYENYN LLNAMLAC A WNSNSTLCVD FYSDRFGKDK ATLNIKRYDG SFIEHDQGLL VDIKNSVVFP ANRIDELVVD AISLKNPGLH ISLLKKDEF AYDLSALNVQ DSPWLIVGKL DGTARIAPVI KWMLPVLQTN DLLLNALCEA DPEQRKKNFN ELIFEIDNNP LQNYCCLLTE YIKKYKMNN GLSLLDLDLF RGISSNYRVV VQLLISSCLS GDSDTIYDIQ EELPFSWGWI PVSIWKDVFQ KCWTYLEKQI N DKTLALHI LQPFIAFMNH RAHIDRRLAP IANMLLTYSE SLPTGCDVLP TVSREQFNEA KQMLLRNPDS FGRISIFPKE LW SSAITPE LKSVFNKLWI EDKYHSRLEK RFNLMLVAAL LTQKDNNLIH QLSALFEFHY QQAPQQLGVI YQYYFEQAGV CH

UniProtKB: UNIPROTKB: A0A0H3JRX1

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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

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1950 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1193665
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 67814
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 83
Output model

PDB-9tud:
CryoEM structure of DruH from Druantia type III

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