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

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Basic information

Entry
Database: PDB / ID: 7kln
TitleMyoviridae Phage XM1 Neck Region (12-fold)
Components
  • Head completion protein, gp1
  • Portal protein
KeywordsVIRAL PROTEIN / Myoviridae / Phage / Baseplate complex
Biological speciesVibrio phage XM1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A1: Portal protein
B1: Portal protein
C1: Portal protein
D1: Portal protein
E1: Portal protein
F1: Portal protein
G1: Portal protein
H1: Portal protein
I1: Portal protein
J1: Portal protein
K1: Portal protein
L1: Portal protein
A2: Head completion protein, gp1
B2: Head completion protein, gp1
C2: Head completion protein, gp1
D2: Head completion protein, gp1
E2: Head completion protein, gp1
F2: Head completion protein, gp1
G2: Head completion protein, gp1
H2: Head completion protein, gp1
I2: Head completion protein, gp1
J2: Head completion protein, gp1
K2: Head completion protein, gp1
L2: Head completion protein, gp1


Theoretical massNumber of molelcules
Total (without water)717,18924
Polymers717,18924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein


Mass: 47018.758 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
#2: Protein
Head completion protein, gp1


Mass: 12746.998 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Vibrio phage XM1 (virus)
Has protein modificationY

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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 material: COPPER / Grid mesh size: 400 divisions/in. / Grid 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 FIELD / 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: 25 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16015 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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