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- EMDB-72764: HSV replication fork complex bound to pritelivir -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72764
TitleHSV replication fork complex bound to pritelivir
Map data
Sample
  • Complex: HSV replisome bound to fork DNA
    • DNA: DNA (25-MER)
    • DNA: DNA (25-MER)
    • DNA: DNA (33-MER)
    • Protein or peptide: UL52
    • Protein or peptide: UL5
    • Protein or peptide: UL8
    • Protein or peptide: UL30
    • Protein or peptide: UL42
  • Ligand: ZINC ION
  • Ligand: Pritelivir
KeywordsHSV / replisome / replication / VIRAL PROTEIN
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / exonuclease activity / helicase activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed RNA polymerase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity ...bidirectional double-stranded viral DNA replication / exonuclease activity / helicase activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed RNA polymerase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity / nucleotide binding / host cell nucleus / DNA binding / ATP binding
Similarity search - Function
DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / Helicase / DNA primase / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol ...DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / Helicase / DNA primase / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / Herpesviridae UL52/UL70 DNA primase / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA polymerase processivity factor / Helicase-primase helicase subunit / Helicase-primase primase subunit / DNA polymerase / DNA helicase/primase complex-associated protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain R-15
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYu Z / Abraham J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of HSV replisome
Authors: Yu Z / Abraham J
History
DepositionSep 18, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72764.png

Downloads & links

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Map

FileDownload / File: emd_72764.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.050157644 - 2.272524
Average (Standard dev.)0.0014346818 (±0.02503604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72764_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_72764_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 : HSV replisome bound to fork DNA

EntireName: HSV replisome bound to fork DNA
Components
  • Complex: HSV replisome bound to fork DNA
    • DNA: DNA (25-MER)
    • DNA: DNA (25-MER)
    • DNA: DNA (33-MER)
    • Protein or peptide: UL52
    • Protein or peptide: UL5
    • Protein or peptide: UL8
    • Protein or peptide: UL30
    • Protein or peptide: UL42
  • Ligand: ZINC ION
  • Ligand: Pritelivir

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Supramolecule #1: HSV replisome bound to fork DNA

SupramoleculeName: HSV replisome bound to fork DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7, #6, #8
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15

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Macromolecule #1: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 7.59389 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DG)(DA)

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Macromolecule #2: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 7.739984 KDa
SequenceString:
(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DA)(DG)(DC) (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DG)(DA)(DT)

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Macromolecule #3: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 10.063456 KDa
SequenceString:
(DT)(DT)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT) (DC)(DC)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DC) (DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DA) (DA)(DT)(DT)(DC)

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Macromolecule #4: UL52

MacromoleculeName: UL52 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 114.558562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSF RVTFCLLGTE VGGTHQARGR TRPMFVCRFE RADDVAALQD ALAHGTPLQP DHIAATLDAE ATFALHANMI L ALTVAINN ...String:
MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSF RVTFCLLGTE VGGTHQARGR TRPMFVCRFE RADDVAALQD ALAHGTPLQP DHIAATLDAE ATFALHANMI L ALTVAINN ASPRTGRDAA AAQYDQGASL RSLVGRTSLG QRGLTTLYVH HEVRVLAAYR RAYYGSAQSP FWFLSKFGPD EK SLVLTTR YYLLQAQRLG GAGATYDLQA IKDICATYAI PHAPRPDTVS AASLTSFAAI TRFCCTSQYA RGAAAAGFPL YVE RRIAAD VRETSALEKF ITHDRSCLRV SDREFITYIY LAHFECFSPP RLATHLRAVT THDPNPAAST EQPSPLGREA VEQF FCHVR AQLNIGEYVK HNVTPRETVL DGDTAKAYLR ARTYAPGALT PAPAYCGAVD SATKMMGRLA DAEKLLVPRG WPAFA PASP GEDTAGGTPP PQTCGIVKRL LRLAATEQQG PTPPAIAALI RNAAVQTPLP VYRISMVPTG QAFAALAWDD WARITR DAR LAEAVVSAEA AAHPDHGALG RRLTDRIRAQ GPVMPPGGLD AGGQMYVNRN EIFNGALAIT NIILDLDIAL KEPVPFR RL HEALGHFRRG ALAAVQLLFP AARVDPDAYP CYFFKSACRP GPASVGSGSG LGNDDDGDWF PCYDDAGDEE WAEDPGAM D TSHDPPDDEV AYFDLCHEVG PTAEPRETDS PVCSCTDKIG LRVCMPVPAP YVVHGSLTMR GVARVIQQAV LLDRDFVEA IGSYVKNFLL IDTGVYAHGH SLRLPYFAKI APDGPACGRL LPVFVIPPAC KDVPAFVAAH ADPRRFHFHA PPTYLASPRE IRVLHSLGG DYVSFFERKA SRNALEHFGR RETLTEVLGR YNVQPDAGGT VEGFASELLG RIVACIETHF PEHAGEYQAV S VRRAVSKD DWVLLQLVPV RGTLQQSLSC LRFKHGRASR ATARTFVALS VGANNRLCVS LCQQCFAAKC DSNRLHTLFT ID AGTPCSP SVPCSTSQPS S

UniProtKB: Helicase-primase primase subunit

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Macromolecule #5: UL5

MacromoleculeName: UL5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 98.823242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ L GQYPYTLT ...String:
MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ L GQYPYTLT SNPASLEDLQ RRDLTYYWEV ILDLTKRALA ASGGEELRNE FRALAALERT LGLAEGALTR LAPATHGALP AF TRSNVIV IDEAGLLGRH LLTAVVYCWW MINALYHTPQ YAARLRPVLV CVGSPTQTAS LESTFEHQKL RCSVRQSENV LTY LICNRT LREYARLSYS WAIFINNKRC VEHEFGNLMK VLEYGLPITE EHMQFVDRFV VPENYITNPA NLPGWTRLFS SHKE VSAYM AKLHAYLKVT REGEFVVFTL PVLTFVSVKE FDEYRRLTHQ PGLTIEKWLT ANASRITNYS QSQDQDAGHM RCEVH SKQQ LVVARNDVTY VLNSQIAVTA RLRKLVFGFS GTFRAFEAVL RDDSFVKTQG ETSVEFAYRF LSRLIFSGLI SFYNFL QRP GLDATQRTLA YARMGELTAE ILSLRPKSSG VPTQASVMAD AGAPGERAFD FKQLGPRDGG PDDFPDDDLD VIFAGLD EQ QLDVFYCHYT PGEPETTAAV HTQFALLKRA FLGRFRILQE LFGEAFEVAP FSTYVDNVIF RGCEMLTGSP RGGLMSVA L QTDNYTLMGY TYARVFAFAD ELRRRHATAN VAELLEEAPL PYVVLRDQHG FMSVVNTNIS EFVESIDSTE LAMAINADY GISSKLAMTI TRSQGLSLDK VAICFTPGNL RLNSAYVAMS RTTSSEFLRM NLNPLRERHE RDDVISEHIL SALRDPNVVI VY

UniProtKB: Helicase-primase helicase subunit

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Macromolecule #6: UL30

MacromoleculeName: UL30 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 136.726891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GAGRGPPPCL RQNFYNPYLA PVGTQQKPTG PTQRHTYYSE CDEFRFIAPR VLDEDAPPE KRAGVHDGHL KRAPKVYCGG DERDVLRVGS GGFWPRRSRL WGGVDHAPAG FNPTVTVFHV YDILENVEHA Y GMRAAQFH ...String:
MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GAGRGPPPCL RQNFYNPYLA PVGTQQKPTG PTQRHTYYSE CDEFRFIAPR VLDEDAPPE KRAGVHDGHL KRAPKVYCGG DERDVLRVGS GGFWPRRSRL WGGVDHAPAG FNPTVTVFHV YDILENVEHA Y GMRAAQFH ARFMDAITPT GTVITLLGLT PEGHRVAVHV YGTRQYFYMN KEEVDRHLQC RAPRDLCERM AAALRESPGA SF RGISADH FEAEVVERTD VYYYETRPAL FYRVYVRSGR VLSYLCDNFC PAIKKYEGGV DATTRFILDN PGFVTFGWYR LKP GRNNTL AQPRAPMAFG TSSDVEFNCT ADNLAIEGGM SDLPAYKLMC FDIECKAGGE DELAFPVAGH PEDLVIQISC LLYD LSTTA LEHVLLFSLG SCDLPESHLN ELAARGLPTP VVLEFDSEFE MLLAFMTLVK QYGPEFVTGY NIINFDWPFL LAKLT DIYK VPLDGYGRMN GRGVFRVWDI GQSHFQKRSK IKVNGMVNID MYGIITDKIK LSSYKLNAVA EAVLKDKKKD LSYRDI PAY YATGPAQRGV IGEYCIQDSL LVGQLFFKFL PHLELSAVAR LAGINITRTI YDGQQIRVFT CLLRLADQKG FILPDTQ GR FRGAGGEAPK RPAAAREDEE RPEEEGEDED EREEGGGERE PEGARETAGR HVGYQGARVL DPTSGFHVNP VVVFDFAS L YPSIIQAHNL CFSTLSLRAD AVAHLEAGKD YLEIEVGGRR LFFVKAHVRE SLLSILLRDW LAMRKQIRSR IPQSSPEEA VLLDKQQAAI KVVCNSVYGF TGVQHGLLPC LHVAATVTTI GREMLLATRE YVHARWAAFE QLLADFPEAA DMRAPGPYSM RIIYGDTDS IFVLCRGLTA AGLTAMGDKM ASHISRALFL PPIKLECEKT FTKLLLIAKK KYIGVIYGGK MLIKGVDLVR K NNCAFINR TSRALVDLLF YDDTVSGAAA ALAERPAEEW LARPLPEGLQ AFGAVLVDAH RRITDPERDI QDFVLTAELS RH PRAYTNK RLAHLTVYYK LMARRAQVPS IKDRIPYVIV AQTREVEETV ARLAALRELD AAAPGDEPAP PAALPSPAKR PRE TPSHAD PPGGASKPRK LLVSELAEDP AYAIAHGVAL NTDYYFSHLL GAACVTFKAL FGNNAKITES LLKRFIPEVW HPPD DVAAR LRAAGFGAVG AGATAEETRR MLHRAFDTLA

UniProtKB: DNA polymerase

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Macromolecule #7: UL8

MacromoleculeName: UL8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 80.005664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTADIVWVE ESVSAITLYA VWLPPRAREY FHALVYFVCR NAAGEGRARF AEVSVTATEL RDFYGSADVS VQAVVAAARA ATTPAASPL EPLENPTLWR ALYACVLAAL ERQTGPVALF APLRIGSDPR TGLVVKVERA SWGPPAAPRA ALLVAEANID I DPMALAAR ...String:
MDTADIVWVE ESVSAITLYA VWLPPRAREY FHALVYFVCR NAAGEGRARF AEVSVTATEL RDFYGSADVS VQAVVAAARA ATTPAASPL EPLENPTLWR ALYACVLAAL ERQTGPVALF APLRIGSDPR TGLVVKVERA SWGPPAAPRA ALLVAEANID I DPMALAAR VAEHPDARLA WARLAAIRDT PQCASAASLT VNITTGTALF AREYQTLAFP PIKKEGAFGD LVEVCEVGLR PR GHPQRVT ARVLLPRDYD YFVSAGEKFS APALVALFRQ WHTTVHAAPG ALAPVFAFLG PEFEVRGGPV PYFAVLGFPG WPT FTVPAT AESARDLVRG AAAAYAALLG AWPAVGARVV LPPRAWPGVA SAAAGCLLPA VREAVARWHP ATKIIQLLDP PAAV GPVWT ARFCFPGLRA QLLAALADLG GSGLADPHGR TGLARLDALV VAAPSEPWAG AVLERLVPDT CNACPALRQL LGGVM AAVC LQIEETASSV KFAVCGGDGG AFWGVFNVDP QDADAASGVI EDARRAIETA VGAVLRANAV RLRHPLCLAL EGVYTH AVA WSQAGVWFWN SRDNTDHLGG FPLRGPAYTT AAGVVRDTLR RVLGLTTACV PEEDALTARG LMEDACDRLI LDAFNKR LD AEYWSVRVSP FEASDPLPPT AFRGGALLDA EHYWRRVVRV CPGGGESVGV PVDLYPRPLV LPPVDCAHHL REILREIE L VFTGVLAGVW GEGGKFVYPF DDKMSFLFA

UniProtKB: DNA helicase/primase complex-associated protein

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Macromolecule #8: UL42

MacromoleculeName: UL42 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 51.207969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRY RWRGPTAAFL SLVDQKRSLL SVFRANQYPD LRRVELAITG QAPFRTLVQR IWTTTSDGEA VELASETLMK R ELTSFVVL ...String:
MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRY RWRGPTAAFL SLVDQKRSLL SVFRANQYPD LRRVELAITG QAPFRTLVQR IWTTTSDGEA VELASETLMK R ELTSFVVL VPQGTPDVQL RLTRPQLTKV LNATGADSAT PTTFELGVNG KFSVFTTSTC VTFAAREEGV SSSTSTQVQI LS NALTKAG QAAANAKTVY GENTHRTFSV VVDDCSMRAV LRRLQVGGGT LKFFLTTPVP SLCVTATGPN AVSAVFLLKP QKI CLDWLG HSQGSPSAGS SASRASGSEP TDSQDSASDA VSHGDPEDLD GAARAGEAGA LHACPMPSST TRVTPTTKRG RSGG EDARA DTALKKPKTG SPTAPPPADP VPLDTEDDSD AADGTAARPA APDARSGSRY ACYFRDLPTG EASPGAFSAF RGGPQ TPYG FGFP

UniProtKB: DNA polymerase processivity factor

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: Pritelivir

MacromoleculeName: Pritelivir / type: ligand / ID: 10 / Number of copies: 1 / Formula: A1BXB
Molecular weightTheoretical: 402.491 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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