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- EMDB-22873: Baseplate Complex for Myoviridae Phage XM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-22873
TitleBaseplate Complex for Myoviridae Phage XM1
Map data
Sample
  • Virus: Vibrio phage XM1 (virus)
    • Protein or peptide: tail tube protein, gp7
    • Protein or peptide: baseplate wedge protein, gp17
    • Protein or peptide: baseplate organization protein, gp11
    • Protein or peptide: baseplate stabilizing protein, gp12
    • Protein or peptide: baseplate wedge protein, gp16
    • Protein or peptide: tail sheath protein, gp6
    • Protein or peptide: tail sheath initiator protein, gp15
KeywordsMyoviridae / Phage / Baseplate complex / 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
DepositionOct 19, 2020-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 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: 2.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kh1
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kh1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22873.png

Downloads & links

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Map

FileDownload / File: emd_22873.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: 2.4 / Movie #1: 2.4
Minimum - Maximum-10.259558 - 13.778262
Average (Standard dev.)0.019130155 (±0.5836957)
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-10.26013.7780.019

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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 tube protein, gp7
    • Protein or peptide: baseplate wedge protein, gp17
    • Protein or peptide: baseplate organization protein, gp11
    • Protein or peptide: baseplate stabilizing protein, gp12
    • Protein or peptide: baseplate wedge protein, gp16
    • Protein or peptide: tail sheath protein, gp6
    • Protein or peptide: tail sheath initiator protein, gp15

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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: tail tube protein, gp7

MacromoleculeName: tail tube protein, gp7 / type: protein_or_peptide / ID: 1 / 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 #2: baseplate wedge protein, gp17

MacromoleculeName: baseplate wedge protein, gp17 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 27.419787 KDa
SequenceString: MSDFLNQYLL YLIKQYYEKP KANAEAQLLI STWETYADFI ANFGNNFDID NAEGEVLDLI GRILDLSRQV NDVIPASFFG FSENPLAKG FTSLENPLRV SAPFFKLTSK VYTDYQLTDT QYRKFLKVKA AKNICSPYLA SDEKISLQQV VFDAFDGRAY V VDGKDQTL ...String:
MSDFLNQYLL YLIKQYYEKP KANAEAQLLI STWETYADFI ANFGNNFDID NAEGEVLDLI GRILDLSRQV NDVIPASFFG FSENPLAKG FTSLENPLRV SAPFFKLTSK VYTDYQLTDT QYRKFLKVKA AKNICSPYLA SDEKISLQQV VFDAFDGRAY V VDGKDQTL RLYVSPSIDD DELRLLINLD ILPRPITFRY IIYGNAEPGV TFGFSNNPGS KSFGSLNNPS RQENGGVFAR FY NG

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Macromolecule #3: baseplate organization protein, gp11

MacromoleculeName: baseplate organization protein, gp11 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 27.675613 KDa
SequenceString: MSLVNGMVES LNNTKSETEI GIGGYRLFAR VRETVNYRNI VPTDTLEDGS SSTDDIINEP ITVSIEGVVS NLFVEERQYP QLVSRDFSA VGEITALLPA KSQQQIQRIS QIDSQIRDAV LAAERAERLA GKPYEFFGNS GNSAKTEQEK FIDFMEALYF S RRPTEVSV ...String:
MSLVNGMVES LNNTKSETEI GIGGYRLFAR VRETVNYRNI VPTDTLEDGS SSTDDIINEP ITVSIEGVVS NLFVEERQYP QLVSRDFSA VGEITALLPA KSQQQIQRIS QIDSQIRDAV LAAERAERLA GKPYEFFGNS GNSAKTEQEK FIDFMEALYF S RRPTEVSV NFRDYKNMAL VSFIPVRDNN TKDTRFTADF QQINYSTLVY TPVSSPSKSV SGKVSDASNK GGQNPESNET GE RSLLSSL VGG

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Macromolecule #4: baseplate stabilizing protein, gp12

MacromoleculeName: baseplate stabilizing protein, gp12 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 13.733485 KDa
SequenceString:
MNLIENITSE YIQTHALEFS RGFAVLTLIY EQAVQMWKMN VVYTRAGDEE PQPPIYGVKL ALSTTHIKHR NWPFDFTVID TTNNGMDPY RADDFETGRC QLYFITPEEM IQVRGVDVQ

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Macromolecule #5: baseplate wedge protein, gp16

MacromoleculeName: baseplate wedge protein, gp16 / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 44.082316 KDa
SequenceString: MSLTFNENGV QTNTFSELRA LLEAGYREIY GTDIVTDQES PDGQRINLET LLRFDIESAF SWLYSNLDPD LNTGDMQQII GKLSGLVLL PASRSQWDVT INMSRAKTLP AGYTITDENN QNWFLDSDVD VLIGDNEVTF LSSLWGSISG ISGSSFTQAT P EIGVVSIS ...String:
MSLTFNENGV QTNTFSELRA LLEAGYREIY GTDIVTDQES PDGQRINLET LLRFDIESAF SWLYSNLDPD LNTGDMQQII GKLSGLVLL PASRSQWDVT INMSRAKTLP AGYTITDENN QNWFLDSDVD VLIGDNEVTF LSSLWGSISG ISGSSFTQAT P EIGVVSIS ASADAIQGRE EETPEQFRLR RQRSTENPAQ STIGSIYAKL AQINGVTDLQ VYDNSSDTPD QITGSSNPDI LN GSEPVTI GAHTMWVVIE GGSLDDIGEV VAKHRLGNTK GSVQVSYIDT LTKPNGDDFQ IVNLHNIDRP VLGDLYVRLT ATQ KVSGSP IDTDAIKNKL SLVDFEIGQY VDADALYQQS LITNSNYNVT DLEVSLNGID WTDGRVFSGY DGKLSISTSN VTIT TVPV

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Macromolecule #6: tail sheath protein, gp6

MacromoleculeName: tail sheath protein, gp6 / type: protein_or_peptide / ID: 6 / 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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Macromolecule #7: tail sheath initiator protein, gp15

MacromoleculeName: tail sheath initiator protein, gp15 / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage XM1 (virus)
Molecular weightTheoretical: 13.392063 KDa
SequenceString:
MRVRTLDDNG DWTFGRGKAD YITSKKAIAQ TVSTRIKSWA NDNPLAMNAN IDWKDLLGRK GTEDTILREI ERVVVQTDGV IRVTELEVI KTEKRVQSIL LSYDTIYDDS ETLEINDL

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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
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 16068
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-7kh1:
Baseplate Complex for Myoviridae Phage XM1

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