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- EMDB-22931: The capsid of Myoviridae Phage XM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-22931
TitleThe capsid of Myoviridae Phage XM1
Map data
Sample
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Minor capsid protein
    • Protein or peptide: Major capsid protein
KeywordsMyoviridae / Vibrio phage / Capsid / HK97 fold / VIRUS
Biological speciesVibrio phage XM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang Z / Klose T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2021
Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine
Authors: Wang Z / Fokine A / Guo X / Jiang W / Rossmann MG / Kuhn RJ / Luo ZH / Klose T
History
DepositionNov 3, 2020-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.37
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kmx
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kmx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22931.png

Downloads & links

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Map

FileDownload / File: emd_22931.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 5.37 / Movie #1: 5.37
Minimum - Maximum-13.564842000000001 - 19.538278999999999
Average (Standard dev.)0.009352921 (±1.2176452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-480-480-480
Dimensions960960960
Spacing960960960
CellA=B=C: 777.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z960960960
origin x/y/z0.0000.0000.000
length x/y/z777.600777.600777.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS-480-480-480
NC/NR/NS960960960
D min/max/mean-13.56519.5380.009

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Supplemental data

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Sample components

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Entire : Vibrio phage XM1

EntireName: Vibrio phage XM1 (virus)
Components
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Minor capsid protein
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Vibrio phage XM1

SupramoleculeName: Vibrio phage XM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2748688 / Sci species name: Vibrio phage XM1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vibrio rotiferianus (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: Minor capsid protein

MacromoleculeName: Minor capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 16.823863 KDa
SequenceString:
MAFNNAVLQE VSDLPAGEVI KASPHNVSAF EVFQNGLIEG RFVKFDAGSI DILDASATPT IAGIAKRKVT GEIGPGVYST SGIEIDQVA EVINFGFATV TVQDAAAPSK YDPVYAINLD SAEAGKATEN SGATGALAVA DCVFWEQKAA NVWLVRMNKF L

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 35.512773 KDa
SequenceString: MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG ...String:
MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG LLNYGFVASG AGDTAANLSG DNLYQAIADL ITDQWAGVFN VETYKADRVV MPDTVYNICA KKILNSNGSE MS VLRALMT NFPTVTFGLT TKARDVGGTS RTTAYSSNRR AMQMRIPTPL NVSSVDQRGF KYYVESYFGV AGLDVIEDTA GRH LTGL

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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 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 19625
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7kmx:
The capsid of Myoviridae Phage XM1

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