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- PDB-7kmx: The capsid of Myoviridae Phage XM1 -

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Basic information

Entry
Database: PDB / ID: 7kmx
TitleThe capsid of Myoviridae Phage XM1
Components
  • Major capsid protein
  • Minor capsid protein
KeywordsVIRUS / Myoviridae / Vibrio phage / Capsid / HK97 fold
Biological speciesVibrio phage XM1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, Z. / Klose, T. / Jiang, W. / Kuhn, R.J.
Funding support United States, 1items
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, M.G. / Kuhn, R.J. / Luo, Z.H. / Klose, T.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-22931
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  • Superimposition on EM map
  • EMDB-22931
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
a: Minor capsid protein
b: Minor capsid protein
c: Minor capsid protein
d: Minor capsid protein
e: Minor capsid protein
f: Minor capsid protein
g: Minor capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)366,35614
Polymers366,35614
Non-polymers00
Water0
1
a: Minor capsid protein
b: Minor capsid protein
c: Minor capsid protein
d: Minor capsid protein
e: Minor capsid protein
f: Minor capsid protein
g: Minor capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)21,981,387840
Polymers21,981,387840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
a: Minor capsid protein
b: Minor capsid protein
c: Minor capsid protein
d: Minor capsid protein
e: Minor capsid protein
f: Minor capsid protein
g: Minor capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.83 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,831,78270
Polymers1,831,78270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
a: Minor capsid protein
b: Minor capsid protein
c: Minor capsid protein
d: Minor capsid protein
e: Minor capsid protein
f: Minor capsid protein
g: Minor capsid protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.2 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,198,13984
Polymers2,198,13984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Minor capsid protein


Mass: 16823.863 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#2: Protein
Major capsid protein


Mass: 35512.773 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vibrio phage XM1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio phage XM1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Vibrio rotiferianus
Virus shellName: capsid / Diameter: 640 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

EM software
IDNameCategory
1EMAN2particle selection
4CTFFINDCTF correction
9PHENIXmodel refinement
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19625 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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