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- EMDB-22896: The Neck region of Phage XM1 (6-fold symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-22896
TitleThe Neck region of Phage XM1 (6-fold symmetry)
Map data
Sample
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: Tail terminator protein
    • Protein or peptide: Collar spike protein
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
KeywordsMyoviridae / Phage / 6-fold neck region / 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 26, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 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: 2.63
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.63
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kjk
  • Surface level: 2.63
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kjk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22896.png

Downloads & links

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Map

FileDownload / File: emd_22896.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 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: 2.63 / Movie #1: 2.63
Minimum - Maximum-9.353338000000001 - 12.435102000000001
Average (Standard dev.)0.018943768 (±0.5961675)
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-9.35312.4350.019

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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: Tail terminator protein
    • Protein or peptide: Collar spike protein
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath 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 / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: Tail terminator protein

MacromoleculeName: Tail terminator protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 18.236037 KDa
SequenceString:
MSQSIINVAR YIRDLLDYDE NLIQFDRKNT QQSDTVTGYI VVNGSGVQNV LSHGSSYDGD AEIMEYSKSE SRLITLEFYG SDAYENAEL FSLLNQSQKA KEVSRGLGLT IYNVSQATDV KQLLGYQYGN RVHVDFNIQY CPSVYVETLR VDASEFEILV D D

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Macromolecule #2: Collar spike protein

MacromoleculeName: Collar spike protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 90.692562 KDa
SequenceString: MSIQVTGIIE GPLGTPSPGI TIRVVSKISY RNTYRLSTED YVTTTGGAYD FQLNEGFHKI LIRYRGASSF TKLGDVSVSD QTPSPITLI NLLESSSPKA LVVKLQELAD EASESAQSAS DDADQVTLDK QQVTLLAQQV SDDADQVALD RSATAQSEVN A AQSATTAQ ...String:
MSIQVTGIIE GPLGTPSPGI TIRVVSKISY RNTYRLSTED YVTTTGGAYD FQLNEGFHKI LIRYRGASSF TKLGDVSVSD QTPSPITLI NLLESSSPKA LVVKLQELAD EASESAQSAS DDADQVTLDK QQVTLLAQQV SDDADQVALD RSATAQSEVN A AQSATTAQ QSADDAAAIV PNLQSQIDDK IDKTQSIIPD VDALFSLGRH EINPTNNNIP GLSGTRSLLH IQNNLGGFQL AA RTVGSEI HVRSADTNSG NIGPWERLYT TGYRPSSYDL VVKDKAEALS VSHQEGLIIG IESCNGARFV SVLPSDSGGL YLG SLPNGN KLRHIPLDGF SLKTIRTSDF EINSGSDVSQ FLIDASTAGY GQVYIDNDCE VTQLCDITGV KYLESLNGAE MLID DLNGR VKCDTDGFEV KGIVFKKSGD YSNTTFEAYL LETNGEKSLA SRCQFVGQWA GYKLQGNDSS ADLCFFSDGT FMLRV GEGV SSCNINRCFF TRGTRRFTEG EQQGDGIKLT AQSSTQGYNE NIIISDCIFY DTYRDCIDGY VGANRLIVKG SIMLNW GAH ALDFKSRVDD NSESPDGGPL TRNVLVDGCM IWKDVVRPDF DLTLAAVVMS VIPGALPVPT SEADVRQNGL RGMELKN TL IAYKGNGSLI SAASTWRTVI DGCTLTDLGQ IGQIIYAPNS WHLKLINSTV NIDPSNINNV KFSSAMNNAE VNDNTFNR L LISTDGMIRT SIKRNKFNGE GVLSRGLNIA SEEVSAVSNE FENFTSFGAQ IFNSASKCRF DFNEIRNCPA PLGIENPSV NTYHSVRGNI SMGSGAFTGL NRITDNGGVA NGNDHVPYS

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Macromolecule #3: Head completion protein

MacromoleculeName: Head completion protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 13.045932 KDa
SequenceString:
MLPNMRSALK MFEQSVLLKS VETIRVDFVD DIIITATPIR AVVQVADKKK LNLDSLDWSK QYIWVHSGSK MEIGQFIEWH GKDFKLVAA GDDYSDYGYN AWYGEETLKP VLVSS

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Macromolecule #4: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 15.665332 KDa
SequenceString:
MSVIVYRNNQ STLTLNGYTF QHLYQGAALV LTPVNAKTAR TNSINGGVSI SGRVDGGVHT LAIMVQKHSP DDKFLNDAKN SQEPVVFDG SMKRAYTESG TLKKATTTLE TGSITTQPTK TDNNQDPDDS RTYVIEFRNS VETF

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Macromolecule #5: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 53.006762 KDa
SequenceString: MASISEVIRV SLQQEGRAIA PDNMNAVGII TGNQGVLSTA DRYRIYRTAA AVASDFGASS QESAFANTFF DTTPNPISAG GVLVIGYWR SASETVAATS ATLVSEQTSE SVLIPLLNAI NDGSFTITVD GGTEQEVTAL DFTGVSELSE VATILNSAIT G ATVSEDNG ...String:
MASISEVIRV SLQQEGRAIA PDNMNAVGII TGNQGVLSTA DRYRIYRTAA AVASDFGASS QESAFANTFF DTTPNPISAG GVLVIGYWR SASETVAATS ATLVSEQTSE SVLIPLLNAI NDGSFTITVD GGTEQEVTAL DFTGVSELSE VATILNSAIT G ATVSEDNG YFKVTSSTTG ATSLLSYLGV ATSGTDISAV LGMNSESGAV LTQGTDQVVL PAETKLEGIT AIKSEVNIKG AM FIDQILD ADIPGIASFA GANNMLVYEV FDTGYLSKNV SNPVWAVKLA GQSNFRCLLS KSGNRKFAAT YMARMHTVLF SGQ NTAITM QLKELSVTAE EYTDTEIANA KTVGLDLLTT IKNEQALLTS GANDFCDNVY NLEAFRDEIQ TNNYNLLKTT STKI PQTDP GMDTIEDDTE KTCEKYVRNG VFAPGTWTRS DFFGDRQQFV DAIAQKGYYV LIGDLADQTT AERQSRVSPV IQIAV KNAG AVHEEDIIIS VNL

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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: 90 % / 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: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10615
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10615
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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