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- EMDB-43111: Pectobacterium phage PhiM1 ejectosome C8 map -

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Basic information

Entry
Database: EMDB / ID: EMD-43111
TitlePectobacterium phage PhiM1 ejectosome C8 map
Map data
Sample
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Other: Internal virion proteins (ejectosome) of Pectobacterium phage PhiM1
KeywordsInternal virion proteins / ejectosome / C8 map / core proteins / VIRUS
Biological speciesPectobacterium phage PhiM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsEruera A / Hodgkinson-Bean J
Funding support New Zealand, 1 items
OrganizationGrant numberCountry
Other private New Zealand
CitationJournal: PNAS Nexus / Year: 2024
Title: Ejectosome of bacteriophage ΦM1.
Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima ...Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima Jorge / Jaekyung Hyun / Hyejin Kim / Bumhan Ryu / Mihnea Bostina /
Abstract: Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a ...Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here, we describe the ejectosome of bacteriophage ΦM1 to a resolution of 3.32 Å by single-particle cryo-electron microscopy (cryo-EM). The core consists of tetrameric and octameric ejection proteins which form a ∼1.5-MDa ejectosome that must transition through the ∼30 Å aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 and 3.23 Å, and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the ΦM1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages.
History
DepositionDec 11, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43111.png

Downloads & links

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Map

FileDownload / File: emd_43111.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.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-0.75758404 - 1.351143
Average (Standard dev.)0.010833766 (±0.059300076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43111_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_43111_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 : Pectobacterium phage PhiM1

EntireName: Pectobacterium phage PhiM1 (virus)
Components
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Other: Internal virion proteins (ejectosome) of Pectobacterium phage PhiM1

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Supramolecule #1: Pectobacterium phage PhiM1

SupramoleculeName: Pectobacterium phage PhiM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Map refined in C8. / NCBI-ID: 1211386 / Sci species name: Pectobacterium phage PhiM1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pectobacterium atrosepticum (bacteria)

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Macromolecule #1: Internal virion proteins (ejectosome) of Pectobacterium phage PhiM1

MacromoleculeName: Internal virion proteins (ejectosome) of Pectobacterium phage PhiM1
type: other / ID: 1 / Classification: other
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
SequenceString: MIWMFAAAAA QMIQGGLQYA QDAKNQRRQN KADQKYNEAV RSASARQITE INTQRSVSRA QTAQALDAAR RQGAGESSA RNLQAAATDT MGASVEQNLQ EVGVQLAAAE GNLMQNAELT ELSLDSSVMN TVDQARNSIR E LSNPLGTD WAATGSAVGQ IGTSMVANKL ...String:
MIWMFAAAAA QMIQGGLQYA QDAKNQRRQN KADQKYNEAV RSASARQITE INTQRSVSRA QTAQALDAAR RQGAGESSA RNLQAAATDT MGASVEQNLQ EVGVQLAAAE GNLMQNAELT ELSLDSSVMN TVDQARNSIR E LSNPLGTD WAATGSAVGQ IGTSMVANKL GGQGWFGGNS GTQQPAPISQ AAPPTRSNNL STRLNV MPV RQPTQGGVQV PGLTGYQSAG VAQPVYRAPQ EEAQGVSQFW QNLLPASVKT AQAAQQTASA KGYLEGQ QD SQQGREKQVR NFFTKEAYEQ GYNSASVNSA LASFQLGLQN TAQQYVNSGK TPEEFNVHVQ QQTNQLLQ E AGAQGLNLND KDWQAWLGSV EHSRNTANAS YQDLNLKRAA VLQEQSWGAR GNAAIADFVT AQQSGDTEQ ALQNVNSFIS SVTHDDSITA ENKIKYTSQF VVNAFANANS TGDMQALTGY VQSLSEFKNM PTDVQTQIMG SAQQYYQQR ASDESVQLYE YNSRVNSVTD YKTLNEAYPM AQYIGTVMQA VQQKKLSPGT GYGMVDAESQ R RLKMQKAE QGQLAYTNGV TISDIAAGTG ESLDKVKGEL TKMYATIGQG YSGGGLQLMQ RGLKSGAQDI TGVGIEMMQQ DAQSLSGIDW RNLKTDADGK PLYPAAVVGS LGNLQAAYQS ALAAGNQVQA NQLLSGLPDP VVYGIRQNVD ARDLADVVGK RAQDIASGKV LALPANMPAD VSITQADVTA GIFDLGLGKD ARNRNMLGIQ SWVFTSDADE KAAQARVSQV NSAMNNEYVY NQQRGSLPAL VGDDLKSWLM GKVASRTVRV KDGTDNGALL VLPEVGDKQK VFGSTDNGII ESALTESVTN FKKQYPQATT VQMDYDPLTQ ELIFQGVNAE NQLGTTRASI PAADFRNTVR GVQNTLTQNG SGTTQGNLNV PGAGFVSFNA GNSFGIQKNV VMGAVNQLVS YEGYTPSKGF SVLGVHPTTG AKLNEDKYVK QATDTPQVAA DKFNMYLNDK VYPLVMPKME QYKNLPGYIQ NNIYNALVET TYHSGNSDVF DKYIQTALYG NVQEIPTFKD TPLFKDAGAG SRRNVDRYQL LGSLVTYRTN NPNLSKMIHL RPDSTAYARS AAVSANPAVG GYVTPDNTVL EGQNPSALVQ AMQKPVASVT DSFKATLSES IGAKALRGVE YASIPTEAGF EPSKALGDSV SQYTADELEF LSDARSSAEL AQRRSQVQDT RNNYDAMGQN MLTTVAASML DVDMVIGGGV GALSKVSRAT RLAVGLSANA ALLGTASYGG TITPLDVVGT SVGIAMSAIP GIRKVAKAEQ VQQGAVRGGV NAAEDAAGTV VPPKDVTVPP VREVPEVQPI KTVADEDYPK IDIDTYSNKE HIEVGRTGGA KTGSLKTTVQ NAVLAVTALG DDLPEGVRAL GRALGASLEA DADVPVVFRS RTGANAQARS AVITEAETGA TRAEIFNPAV GGTLSDHVRG MSTYEKTILL HEAAHAKTGR SIRAVESGAV SDGVVYEAVQ RIKEIQWYVK ANVELPPLGK GAKYNVDYGL SDTHEFISQL FNSEHFRDAL RSVKMPGSDG TLLSNLMKRV VTLFTGKAPE GNAFDATLQA FDNLLSQPTT PADVFLNAPK ATPDLQSKVL QAPNVIEMNN KVMGALNRNF SLYERLKSFG YKASTLADQL VVDATGTEAN SAAHHARAAH LASNVSIVQV DDAFRQALSA DWPLVQRLRH PVLYREAQRD LSQKVYQQLA ENHDRFLKGQ SIQPSNDPRV NSMVDAFVNS NWAKDELARV KGAGINGADA VRESPYYLPR QHSGNKLNDF MRNNRQVTKD DIVGMYTEQF SRMFQQNGIT PETARKLGAK MFDNMQDQAA HVQGYRQSIA GMSYDDIENT LEALGASDPT ITAFLDAVKG SGEQANKVRN LRGRAEFDMT AQYTTKSGDM ISPSMFVNND VMGLMEGYSR RMSGRVGLAK AGFPDLRDAV KAIDEAAAEA QDPAAALHAF DNTMNQILGY PTGEDVPDIL RSASIIGGAL NLANSGIYQL ADMSLMLQQF GITKTLKAFG STAFGRNAMD VAKSAEFGSR LQDVIEARHV LSGKYRSVLT HLEDNRDIGS LGVAHRYVQQ MGQGTRFVNG MEFIRRGQAK LVSGLIADTV DDAIAGNASA VTAMERFGLN QQLLDELRKA TAANPDMRKW PDSVRMDIEA VTHNMADSIV LENRLGEIPA WMQFSSVGKV ILPYMTFVAG AWNKILRRTA KLDGATGVAI ALAYQMPLVT LSSATSIAIS GKPVTPESVA QRALVQVPMM SWAGFAVDFW ANGASNNLAA LALVDRMHAA MSSIASGETN PESLIKAVPF LSILPGMRLM GASLADDDE

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36765 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17729
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

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