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- EMDB-65907: Cryo-EM structure of helicase DruE in the Druantia anti-phage sys... -

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Basic information

Entry
Database: EMDB / ID: EMD-65907
TitleCryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism
Map dataPrimary Map: The EMReady2-processed map in CCP4 format, aligned to the coordinate frame of the fitted model
Sample
  • Complex: DruE-DNA-ADP complex
    • Protein or peptide: Helicase
    • DNA: forked DNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsSF2 Helicase / DNA-dependent ATPase / DNA-binding / DNA BINDING PROTEIN / HYDROLASE
Function / homology
Function and homology information


3'-5' DNA helicase activity / interstrand cross-link repair / nucleotide-excision repair / nucleic acid binding / ATP binding
Similarity search - Function
YjiV N-terminal domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPseudomonas protegens Pf-5 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsHou J / He YX / Gui L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971422 China
CitationJournal: To Be Published
Title: Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism.
Authors: Hou J / He YX / Gui L
History
DepositionAug 19, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65907.png

Downloads & links

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Map

FileDownload / File: emd_65907.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map: The EMReady2-processed map in CCP4 format, aligned to the coordinate frame of the fitted model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.153
Minimum - Maximum-0.10302466 - 20.241287
Average (Standard dev.)0.003266082 (±0.48423874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Original Map: The unprocessed CryoSPARC output map is...

Fileemd_65907_additional_1.map
AnnotationOriginal Map: The unprocessed CryoSPARC output map is provided as an additional EM map (raw map) for reference and validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map: The unprocessed CryoSPARC output map is...

Fileemd_65907_half_map_1.map
Annotationhalf Map: The unprocessed CryoSPARC output map is provided as an additional EM map (raw map) for reference and validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map: The unprocessed CryoSPARC output map is...

Fileemd_65907_half_map_2.map
Annotationhalf Map: The unprocessed CryoSPARC output map is provided as an additional EM map (raw map) for reference and validation
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-DNA-ADP complex

EntireName: DruE-DNA-ADP complex
Components
  • Complex: DruE-DNA-ADP complex
    • Protein or peptide: Helicase
    • DNA: forked DNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DruE-DNA-ADP complex

SupramoleculeName: DruE-DNA-ADP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas protegens Pf-5 (bacteria)
Molecular weightTheoretical: 463 KDa

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Macromolecule #1: Helicase

MacromoleculeName: Helicase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas protegens Pf-5 (bacteria)
Molecular weightTheoretical: 221.376172 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SQDPMVLDPI GGFHRIQDFF ISYVETSFRI SNPTAAEARR ALLKTCGILA TEPFIEPVLR YESSDKNLED LIEEEDGTL QPLSLEGRKA FVELALSGLF DGEPSKGLLR RKSAYAPYRH QISMLERGVR AGCPGIVTSG TGSGKTESFM L PVLAALAN ...String:
MGSSHHHHHH SQDPMVLDPI GGFHRIQDFF ISYVETSFRI SNPTAAEARR ALLKTCGILA TEPFIEPVLR YESSDKNLED LIEEEDGTL QPLSLEGRKA FVELALSGLF DGEPSKGLLR RKSAYAPYRH QISMLERGVR AGCPGIVTSG TGSGKTESFM L PVLAALAN EAVDWPKPGV NYLQEHWWQT PKSRWSPRRA GEKRPAAVRA LVLYPMNALV EDQMVRLRKT LDAEEAHAVM DE RFTGNRL FFGQYTSATP VTGYEQHPRL AGDKQEVKRR ARRIARLRKA MQNFQRDQDA ARRFDADVQS DGKASVEKTR YIF PSVDGG EMVSRWDMHA APPDILVTNA SMLGAMLSRE IEDAIFEKTR EWLMSDEDAY FYLIFDELHL IRGSAGTEIA LLIK SLIQR LGLDQPEHCY KLRLLASSAS LPMEGVEGVQ SRTYLRDLFA PFGTSSRPND LGSIDPSFWS KCIIQGVVHI PPVQQ CGIP AEPFVQLMKA ALEGKDNFVG QLDRTPALDA AIVQAAKVLG ITETEQTTLV KQLAETAASL LTHACKNDGT IRATTP RSI AARIFAPATG DTELALRGLL LARSLPESNQ SAVKVAVATP AFRVHTFIRN IEGLFASVAP GEPDVAFDNF SVERGTS HS APVEGQRRGH RLFELLYCEA CGDLFVGGQR GQSSGSMNAT ELLPSAANLE HLPERPGAEY YDDMTLDEFA VFWPRRGD W IGSDKGYDQW EPAHLNPDTG IVEIGEIAKE GNIAGYLYYQ TKAAVSKDKE RSTQQPSAQP FCCPKCGTDY SNRPDTNRS RSPIRAFRTG VTKSSQLVAT ELFELLHAIG AEPKGIVFSD SRQDAAAQAM EIERLHLRDL RREVLVTAAR SYVKDASIEV LTSKEIIER LIKAETAGDK DEVIRLSELL KKQTVACGPK TRKVKLDKLL EFGNDGSIGR ITAELVRLGI SPYKHSSSND A KELPWYRE FEKNGDLIAY DHTLSYTQTV GLNKDIVEGQ YELIDDVIFA NTFFALEETG LAYPCLPMDE DDQALDAWLR VF ASAYRVK DNRYFDKNKV KLWQKGPDVT NGRIKKVARA LYGETRYGDE LTRVLGEFER LGHRGGLFNI GKLALKVTEP GDD FWRCSN CERVHLHRGL GVCTRCVAPL HEPSGKVEAL WETNFLGRRI VRGERDGVGR FRLRVEELTG QTDDFSDRLR KFKG IFVDD VSELEKLASE IDMLSVTTTM EVGIDIGALQ TVYQANMPPQ RFNYQQRVGR AGRRGQAFSF VVTFCRGRSH DAYYF AHPQ AITGDPPPPP FLATGHDAIP MRLLRKTWLR AAFKQLREQC AKLGESFPGD LLIPPDVHGE YVTTKDYYHS QEIDWP IRL SEALKQTQSV RDRFIETATF DQEQRQRLYA KSSIDLLLKE INDQRPHAPD DEVGLARFLA ERGLLPMYGM PTRVRNL YV GLRESKTQSD HSEYEWSMMD RDLDLAVFEY APGAVLVKDK KKHRVIGFTG NLTDPQAQGR SIEGIRSVTD WSESQTYV A ICPACGSASQ SKQAPEGPLA CNDCQAPIPK ESFLHYVTPA AFRTDFLPKD ELDEFERMSL RTVATVLREG DCFNYRALT VRSGAGVTIL QLNDGPTDGK NDGQRFTVDL VQDQRVPVPF STQRPAIDGI QAIESSWRRS HISPRWSQPL SEQRFGLISQ KETDSIHLE LTRFDKRLTL DMVSRKGDFM HLPTRAAAIS ATQILVNKAA LALDVSPDEF EALEPRLRSG HPMLQIADAL I NGSGLSRR LGEPASDGPT PLLVDLLHEI LEKPNVWPLQ DFLRTGAEGP HAAQCQTSCY RCIQRYGNRR YHGLLDWRLG LA YLRTLVT PAYACGLTPG DDKYPEIQGW RERASQLADD VEAMRKGTIR TERLPHSDLP CLIEQKDGVE LWRAVVIHPL WRH SEPGVM RDLLGADWSP SLRYLDTFEL ERRPLRRLAA LKQEGSWSHP QFEK

UniProtKB: Helicase

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Macromolecule #2: forked DNA

MacromoleculeName: forked DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.49073 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DT) (DC)(DG)(DA)(DT)(DG)(DA)(DG)(DC)(DA)(DC) (DT)(DG)(DC)(DT)(DA)(DT)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DC) (DT) (DC)(DA)(DT)(DC)(DG)(DA) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DA)(DT) (DC)(DG)(DA)(DT)(DG)(DA)(DG)(DC)(DA)(DC) (DT)(DG)(DC)(DT)(DA)(DT)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DC) (DT) (DC)(DA)(DT)(DC)(DG)(DA)(DT)(DG) (DA)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DC)(DG) (DA)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DT) (DT)(DT)(DT)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mM/LNaClsodium chloride
20.0 mM/LTris-HclTRIS hydrochloride

Details: 150mM NaCl,20mM Tris-HCL
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EPU / Number images used: 73269
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial local fitting was done using Chimerax
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9wdv:
Cryo-EM structure of helicase DruE in the Druantia anti-phage system elucidates its anti-phage mechanism

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