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- PDB-7eel: Cyanophage Pam1 capsid asymmetric unit -

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Basic information

Entry
Database: PDB / ID: 7eel
TitleCyanophage Pam1 capsid asymmetric unit
Components
  • Cement (decoration) proteins
  • Major capsid proteins
KeywordsVIRUS / Major capsid and cement proteins
Biological speciesunidentified (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsZhang, J.T. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Structure / Year: 2022
Title: Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1.
Authors: Jun-Tao Zhang / Feng Yang / Kang Du / Wei-Fang Li / Yuxing Chen / Yong-Liang Jiang / Qiong Li / Cong-Zhao Zhou /
Abstract: Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near- ...Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near-atomic-resolution structure of a freshwater short-tailed cyanophage, Pam1, which comprises a 400-Å-long tail and an icosahedral capsid of 650 Å in diameter. The outer capsid surface is reinforced by trimeric cement proteins with a β-sandwich fold, which structurally resemble the distal motif of Pam1's tailspike, suggesting its potential role in host recognition. At the portal vertex, the dodecameric portal and connected adaptor, followed by a hexameric needle head, form a DNA ejection channel, which is sealed by a trimeric needle. Moreover, we identify a right-handed rifling pattern that might help DNA to revolve along the wall of the ejection channel. Our study reveals the precise assembly pattern of a cyanophage and lays the foundation to support its practical biotechnological and environmental applications.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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-31078
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  • Superimposition on EM map
  • EMDB-31078
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid proteins
B: Major capsid proteins
C: Major capsid proteins
D: Major capsid proteins
E: Major capsid proteins
F: Major capsid proteins
G: Major capsid proteins
H: Cement (decoration) proteins
I: Cement (decoration) proteins
J: Cement (decoration) proteins
K: Cement (decoration) proteins
L: Cement (decoration) proteins
M: Cement (decoration) proteins
N: Cement (decoration) proteins


Theoretical massNumber of molelcules
Total (without water)372,47214
Polymers372,47214
Non-polymers00
Water0
1
A: Major capsid proteins
B: Major capsid proteins
C: Major capsid proteins
D: Major capsid proteins
E: Major capsid proteins
F: Major capsid proteins
G: Major capsid proteins
H: Cement (decoration) proteins
I: Cement (decoration) proteins
J: Cement (decoration) proteins
K: Cement (decoration) proteins
L: Cement (decoration) proteins
M: Cement (decoration) proteins
N: Cement (decoration) proteins
x 60


Theoretical massNumber of molelcules
Total (without water)22,348,313840
Polymers22,348,313840
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: Major capsid proteins
B: Major capsid proteins
C: Major capsid proteins
D: Major capsid proteins
E: Major capsid proteins
F: Major capsid proteins
G: Major capsid proteins
H: Cement (decoration) proteins
I: Cement (decoration) proteins
J: Cement (decoration) proteins
K: Cement (decoration) proteins
L: Cement (decoration) proteins
M: Cement (decoration) proteins
N: Cement (decoration) proteins
x 5


  • icosahedral pentamer
  • 1.86 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,862,35970
Polymers1,862,35970
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid proteins
B: Major capsid proteins
C: Major capsid proteins
D: Major capsid proteins
E: Major capsid proteins
F: Major capsid proteins
G: Major capsid proteins
H: Cement (decoration) proteins
I: Cement (decoration) proteins
J: Cement (decoration) proteins
K: Cement (decoration) proteins
L: Cement (decoration) proteins
M: Cement (decoration) proteins
N: Cement (decoration) proteins
x 6


  • icosahedral 23 hexamer
  • 2.23 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,234,83184
Polymers2,234,83184
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
Major capsid proteins


Mass: 39379.066 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) unidentified (others)
#2: Protein
Cement (decoration) proteins


Mass: 13831.203 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) unidentified (others)
Source detailsThe source organism is a short-tailed cyanophage which was separated and sequenced by the author.

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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: Pam1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: unidentified (others)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Pseudanabaena mucicola
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21210 / Symmetry type: POINT

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