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- EMDB-22917: Myoviridae Phage XM1 Neck Region (12-fold) -

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Basic information

Entry
Database: EMDB / ID: EMD-22917
TitleMyoviridae Phage XM1 Neck Region (12-fold)
Map data12 fold average for phage XM1 neck
Sample
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Head completion protein, gp1
KeywordsMyoviridae / Phage / Baseplate complex / VIRAL PROTEIN
Biological speciesVibrio phage XM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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
DepositionOct 30, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kln
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kln
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22917.png

Downloads & links

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Map

FileDownload / File: emd_22917.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation12 fold average for phage XM1 neck
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 512 pix.
= 414.72 Å		0.81 Å/pix.
x 512 pix.
= 414.72 Å		0.81 Å/pix.
x 512 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-13.154527 - 20.011960999999999
Average (Standard dev.)0.004918425 (±0.5480154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 414.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-13.15520.0120.005

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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: Portal protein
    • Protein or peptide: Head completion protein, gp1

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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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 47.018758 KDa
SequenceString: MKFFDGVKDV LSGLINRRNS MARNRVSHRY LSDEEMRVMY KAGLMSKIIR LKAGYALNDT LKFESTQDQE IYKKRLSKHV KNATKFMLG FGRGVIVVFK NGDDLSKPLE RGVDPKLLKI RVFSGDIAKG NNPDNDLRSE RYYKPKNYTI KGHTIHWTRV V DFTYYMPS ...String:
MKFFDGVKDV LSGLINRRNS MARNRVSHRY LSDEEMRVMY KAGLMSKIIR LKAGYALNDT LKFESTQDQE IYKKRLSKHV KNATKFMLG FGRGVIVVFK NGDDLSKPLE RGVDPKLLKI RVFSGDIAKG NNPDNDLRSE RYYKPKNYTI KGHTIHWTRV V DFTYYMPS ENELPDYYYG GMSESELIYE QFINDSVVQR ASGSIIEKAS TFVYKIKGYK QLIQAKKEED IIKYVSTCED GR SIYGGLI TDADDEVSTL TQSLTDLDKV DNVTLRRIAM VTGLGMTVLI GEQASGLNAS GEKERQGFQD TIENLQSDYL EDP LNRLAE IFQLGFIEFK DNQGQSANER VEYDKKAVDV AKVLWELGED YGAYLKDKDV VQADDWDNFW KEKDENSEVD ESLP LGDLF SSGDVNG

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Macromolecule #2: Head completion protein, gp1

MacromoleculeName: Head completion protein, gp1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 12.746998 KDa
SequenceString:
MALIDDFKAR FPNLDGSLVD ALVPVYENNY SCYYGGSYEN DCDKEAILLL IAHLVVTDPS YSGDESSSRA VASQSVGSVS VSFVAGSTG SDWTNWLNST RYGQLFLMVT SNNMGPSFA

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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 / Material: COPPER / Mesh: 400 / 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
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 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: 2.0 µm / Nominal defocus min: 0.5 µm
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 16015
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7kln:
Myoviridae Phage XM1 Neck Region (12-fold)

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