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- EMDB-56256: CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - d... -

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Basic information

Entry
Database: EMDB / ID: EMD-56256
TitleCryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 5
Map data
Sample
  • Complex: DruE:ATPgammaS:DNA
    • Protein or peptide: DEAD/DEAH box helicase
    • DNA: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ZINC ION
KeywordsBacterial helicase / Druantia / Immune System / NTPase / DNA binding protein / DExH box / HYDROLASE
Function / homology:
Function and homology information
Biological speciesEscherichia coli O157:H7 str. EDL933 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_56256.png

Downloads & links

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Map

FileDownload / File: emd_56256.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 288 pix.
= 319.488 Å		1.11 Å/pix.
x 288 pix.
= 319.488 Å		1.11 Å/pix.
x 288 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0 - 0.2928533
Average (Standard dev.)0.00270024 (±0.013013061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56256_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_56256_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 : DruE:ATPgammaS:DNA

EntireName: DruE:ATPgammaS:DNA
Components
  • Complex: DruE:ATPgammaS:DNA
    • Protein or peptide: DEAD/DEAH box helicase
    • DNA: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ZINC ION

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Supramolecule #1: DruE:ATPgammaS:DNA

SupramoleculeName: DruE:ATPgammaS:DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)

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Macromolecule #1: DEAD/DEAH box helicase

MacromoleculeName: DEAD/DEAH box helicase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)
Molecular weightTheoretical: 237.744781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAEFMDVQQL HYAPLLNQLH QRAVRSVVSQ LALRSKSLTH YLESQYFQPP GQEGSLLADP VFESTFGWMP ADETMEDLRD KLISSPLVD ALSKAPVPFR HQLTAWRTIL EDKKSLLVSS GTGSGKTECF MVPVLEDLIR QQKSTRQSLT GTQAIFLYPL N ALINSQQE ...String:
GAEFMDVQQL HYAPLLNQLH QRAVRSVVSQ LALRSKSLTH YLESQYFQPP GQEGSLLADP VFESTFGWMP ADETMEDLRD KLISSPLVD ALSKAPVPFR HQLTAWRTIL EDKKSLLVSS GTGSGKTECF MVPVLEDLIR QQKSTRQSLT GTQAIFLYPL N ALINSQQE RLREWTRGFK GKIRFALYNG ETRHTKYEIQ EDQLKVPEQA LSREAIYEAP PSIMVTNTTM LEYMLIRRKD AP IIEKSQG MLKYIVLDEA HSYIGSQAAE LALLLRRVMQ AFNVGPGTDK PVQIIATSAT IGEDSPEGNK ELAKFVADLA GVT ERDVKV VRGYRQIPRV SESLIRHEYP TSLTSLKSLS PQDLYQQLCH YRVAQQLRQA LTHPGRQAVR LSELLNVARR TWPD INHRE LLQLLDLMAR SREGELAFTP LRMHGFIRTL AGLWACSNKQ CSHKAHELNQ SDWPFGQVWF EQRQYCDCGA PVFEV LRCS GCGSAYLSAK EEMRGDGTNW LVAQPAAAEV DEFALDVDVY SEDEDNDELD NNSQFDRLIA SDGEKYIISL EETTAG KID SEAQKHYEIN LLRPESRGEG RNNSFACVCC GDTQRKNNPL FRPLRLGAPF FLNEIIPTLL EFSPLPQTRE EQLGPFN GR RLLTFTDSRQ GTARISARLQ QDADKATLRA LCYQELANIT EPSAKLSPAH CALLEKVISQ FSVLPLKNSI DALKKAMA A NEELSPTDIQ ALKIIEPMVS SLSTEHAEAM QILQANSGNQ QKKTMSWQTL SEQLVGSVDL ADRMRGSFKE LSGLDLTKQ QFADFCLYSE FGRRPKNAWT LESLGLVAIH YPFIDKVTTC PQDWKTLLPD PDKQLAEWRN LLKITLDFFI RENSAVFYEN EQYPRWMGA RFPVKMLQGP DKKNKGQKRD QLWPQIRDRH YNRVIKLLIA VFPAIQPEQA HWKSLVNHLM IEVWDAIRPC L RQFESGYQ LDIKQQAEFY SPKQVWRCPY TRRALDVTLL GYSPYLPGSK EIAPEKAVLI EMPELPVRHW RLSGGGEIAR EE RLEWLES NALIQHAREE GLWSTRSDRL ALKDSWYRLE EHSAQRTPEQ NQFNEKQFKS GKVNVLNCST TMEMGVDIGG MSL VAMNNV PPAPANYLQR AGRAGRRGES ASAAITLCKN TAHGMEVFKD PLWAFNTTAS APRVRFGSSS IVQRHVNALV LGLF LRAEV PDATKLSCKW FFEGDESQCL RFLHWLNHQA DQLADKLKRL TQGTVLMSLT ATQLLTRTQA MMQQVDIRWR SQLAI LLEN IEALKADNSA WEETPAGKAI AYQLRDYRGA YLFSKLISEA FLPGHGFPVG VVNFNYLTAD ELEKRRAIKA TQADPN EGG ESFSRRIEKL PSRDLPTALR EYAPGADVVL GGKVYRSSGI MLGKVLASGQ ELSGDHHIPW FWHCRKCGAG ATSTTHP VE CSHCKADIQQ LDVKRYLQPV GFATDIRYQA HNDVSMPAQL PWKDPRVLVP SSVWVSLPDA GLGRYRFSHS GELFHFSE G EFGHGYAICL SCGRAESQTQ PQRTPENLKN PERENTHYLL RGGSNDRQGS NKLCHGHVHK DLWLGYSSRT DMVELQLND DNGLLIRDEV AARSLAVALR EGLAHKLGIE NTELGVTTQQ ARDINGYTGY SIFIYDNNAG GAGYAVQLID HWADVFNYAR KLLDCSCDK FCHHCLLSYD SQHYVNRLDR HHALTLLTNV RLQRLNLAPE YQYFGDGSRV ETNPLSLRIA QCLNSEIYDS C SLVLAGPQ EQWDFAQWPL FKELLQFASS GGNVELLVAT PLANLTDSSR HQLSALAAMP GGRLQVKSIA TAQLMQGKGR WL AQVTREG QSQQWAADDS ATVAPGELWG QSASSPVVTL KGTSGKTFSG QTLSAEDLLP ALPTGAVRIN LCEQLDGPLE GFG SRFWSL VTQQHAGWKQ AFTRHKEITH VEYSDRYLNS PFTARLLGEI LTELVEQGMA ERASLTVCVK KLDYNSRQHD ALYN AWLNE EDRQQVVTTL LEEGYLGPAW PGAISWLTGD NQSTEHGREL TVTFSDGSQH YVLLDMGLSY WRCIEDTFFD FALRV PQQV ERLANTRARA VAPGNDLRSY IIAG

UniProtKB: UNIPROTKB: A0A4P8BDA5

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Macromolecule #2: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP...

MacromoleculeName: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.191942 KDa
SequenceString:
(DA)(DT)(DC)(DG)(DA)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DC) (DC)(DA)(DG)(DA)(DC)(DC)(DA)(DA)(DA) (DT)

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Macromolecule #3: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')

MacromoleculeName: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.249995 KDa
SequenceString:
(DT)(DA)(DA)(DA)(DC)(DC)(DA)(DG)(DA)(DC) (DC)(DG)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DA)(DC)(DT)(DA)(DT)(DC)(DG)(DA) (DT)

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 10 / 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

Concentration8 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: 2724 / Average exposure time: 40.57 sec. / 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: 96000
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

Particle selectionNumber selected: 660861
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21364
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9tuc:
CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 5

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