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- PDB-7eea: Cyanophage Pam1 tailspike receptor-binding domain -

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Basic information

Entry
Database: PDB / ID: 7eea
TitleCyanophage Pam1 tailspike receptor-binding domain
ComponentsShort-tailed cyanophage tailspike receptor-binding domain
KeywordsVIRAL PROTEIN / Tailspike receptor-binding domain
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.671 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 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
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.identifier_ORCID / _citation_author.name
Revision 1.2Jun 7, 2023Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-tailed cyanophage tailspike receptor-binding domain
B: Short-tailed cyanophage tailspike receptor-binding domain
C: Short-tailed cyanophage tailspike receptor-binding domain


Theoretical massNumber of molelcules
Total (without water)211,1533
Polymers211,1533
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-17 kcal/mol
Surface area51850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.580, 241.272, 176.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Short-tailed cyanophage tailspike receptor-binding domain


Mass: 70384.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.34M sodium phosphate monobasic monohydrate, 0.06M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.671→50 Å / Num. obs: 72867 / % possible obs: 98.5 % / Redundancy: 12.3 % / CC1/2: 0.893 / Net I/σ(I): 15.7
Reflection shellResolution: 2.671→2.8 Å / Rmerge(I) obs: 0.857 / Num. unique obs: 72556

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.671→19.439 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 3583 4.94 %
Rwork0.2098 68973 -
obs0.2121 72556 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.79 Å2 / Biso mean: 48.8713 Å2 / Biso min: 18.17 Å2
Refinement stepCycle: final / Resolution: 2.671→19.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14410 0 0 236 14646
Biso mean---45.87 -
Num. residues----1935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.671-2.70580.31841070.2617184368
2.7058-2.74280.29821320.25862706100
2.7428-2.78180.28541270.2592702100
2.7818-2.82320.30551380.26222703100
2.8232-2.86720.31551440.24632697100
2.8672-2.91410.31251280.25022711100
2.9141-2.96410.3271440.25722691100
2.9641-3.01780.29631490.24552732100
3.0178-3.07570.29131370.23632700100
3.0757-3.13820.29451180.23042710100
3.1382-3.20610.29361500.23442701100
3.2061-3.28040.34191330.22962707100
3.2804-3.3620.28161610.2222268199
3.362-3.45240.25551320.2155269899
3.4524-3.55340.22961300.1996264898
3.5534-3.66740.24291330.1848267897
3.6674-3.79750.23981270.1887263997
3.7975-3.94840.23371600.1796262196
3.9484-4.12640.22921410.1923264997
4.1264-4.34170.20541340.1759261295
4.3417-4.61030.19661480.1783245891
4.6103-4.96080.20191460.173255493
4.9608-5.450.27831250.2092274699
5.45-6.2160.24651230.2185277099
6.216-7.74810.26941670.22582758100
7.7481-19.4390.2451490.209285899

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