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- EMDB-35175: Portal-tail complex structure of the Cyanophage P-SCSP1u -

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Basic information

Entry
Database: EMDB / ID: EMD-35175
TitlePortal-tail complex structure of the Cyanophage P-SCSP1u
Map data
Sample
  • Virus: Prochlorococcus phage P-SCSP1u (virus)
    • Complex: The portal-tail complex of cyanophage P-SCSP1u
      • Protein or peptide: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
      • Protein or peptide: Adaptor protein(gp22) of the cyanophage P-SCSP1u
      • Protein or peptide: Fiber protein(gp 28) of the cyanophage P-SCSP1u
      • Protein or peptide: Portal protein(gp 16) of the cyanophage P-SCSP1u
KeywordsWhole virus / Capsid / cyanophage / T7-like virus / VIRUS
Biological speciesProchlorococcus phage P-SCSP1u (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsLiu H / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses.
Authors: Lanlan Cai / Hang Liu / Wen Zhang / Shiwei Xiao / Qinglu Zeng / Shangyu Dang /
Abstract: Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria ...Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses.
History
DepositionJan 19, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35175.png

Downloads & links

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Map

FileDownload / File: emd_35175.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 256 pix.
= 435.2 Å		1.7 Å/pix.
x 256 pix.
= 435.2 Å		1.7 Å/pix.
x 256 pix.
= 435.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.051198147 - 0.09941386
Average (Standard dev.)0.0012921147 (±0.0053072474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35175_msk_1.map
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Half map: #2

Fileemd_35175_half_map_1.map
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Half map: #1

Fileemd_35175_half_map_2.map
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Sample components

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Entire : Prochlorococcus phage P-SCSP1u

EntireName: Prochlorococcus phage P-SCSP1u (virus)
Components
  • Virus: Prochlorococcus phage P-SCSP1u (virus)
    • Complex: The portal-tail complex of cyanophage P-SCSP1u
      • Protein or peptide: Nozzle protein(gp 23) of the cyanophage P-SCSP1u
      • Protein or peptide: Adaptor protein(gp22) of the cyanophage P-SCSP1u
      • Protein or peptide: Fiber protein(gp 28) of the cyanophage P-SCSP1u
      • Protein or peptide: Portal protein(gp 16) of the cyanophage P-SCSP1u

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Supramolecule #1: Prochlorococcus phage P-SCSP1u

SupramoleculeName: Prochlorococcus phage P-SCSP1u / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1, #4 / NCBI-ID: 2914505 / Sci species name: Prochlorococcus phage P-SCSP1u / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Prochlorococcus (bacteria)

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Supramolecule #2: The portal-tail complex of cyanophage P-SCSP1u

SupramoleculeName: The portal-tail complex of cyanophage P-SCSP1u / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4, #1
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)

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Macromolecule #1: Portal protein(gp 16) of the cyanophage P-SCSP1u

MacromoleculeName: Portal protein(gp 16) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)
Molecular weightTheoretical: 62.460434 KDa
SequenceString: MKTRLTNNVD RQSALYGSSG GTAAQRYEQL RVDRNSPLKR ARDCSKVTIP GLIEDENYGD AGRLDTPYQS SGARGVGHMT SKLAVTLFP TNEHFFKLEI DSLAILASDQ NPEMITEFDS ALVKVEQAVM RMFETIGGRA AMHEALKHLL VGGNVLLYVS D EGIKVIHL ...String:
MKTRLTNNVD RQSALYGSSG GTAAQRYEQL RVDRNSPLKR ARDCSKVTIP GLIEDENYGD AGRLDTPYQS SGARGVGHMT SKLAVTLFP TNEHFFKLEI DSLAILASDQ NPEMITEFDS ALVKVEQAVM RMFETIGGRA AMHEALKHLL VGGNVLLYVS D EGIKVIHL DSYVLCRDPM GNVTEIVVEE EIFKDALPEE YLDEEDDDDD DMGKKMVKIY TCIKFMDDQC HWYQEIKGKE VP GTHGKCA ADVAPWIALR QDRVDSEMYG RSYVEQYYGD LLALENLYKA ILEASASLSK VLFLCNPNGT TRPRTLSQAS NGS IVQGNA ADVTVLQAAG KSQDLQIANQ TIERIENRLA FAFMLNTAIQ RPGERVTAEE IRYMAQELDA GISGLYSILS RELQ LPLVR RLIHILRRKR KLPDFPRSEV TGEPLIKEKA VTGIEAIGRG DDRNKLIDFI TTANQALGPQ AMTQFLNVEE ALRRL AASG SIDTTNLVKT KAQLQQEAAA QAEAEQQAQQ QQLLETGIKS PAMAQAVKNF QGADPERAAQ ALSAITSETG GIDADQ LTE AV

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Macromolecule #2: Nozzle protein(gp 23) of the cyanophage P-SCSP1u

MacromoleculeName: Nozzle protein(gp 23) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)
Molecular weightTheoretical: 87.444898 KDa
SequenceString: MPLISSSIPN LINGVSQQPA ALRLASQAEE VINCMPSPVE GLKKRPPMQH IKKLFAGSAG TGRPFTHIVD RDGVIRYLIF IQDNAIKVF DLDGNAQTVS TPNGTSYLNI TGEPSSTFRV ASIADFTFIV NREKTVAMDT TNKSYNWGTK SMVFIKSADF S TTYRVKLN ...String:
MPLISSSIPN LINGVSQQPA ALRLASQAEE VINCMPSPVE GLKKRPPMQH IKKLFAGSAG TGRPFTHIVD RDGVIRYLIF IQDNAIKVF DLDGNAQTVS TPNGTSYLNI TGEPSSTFRV ASIADFTFIV NREKTVAMDT TNKSYNWGTK SMVFIKSADF S TTYRVKLN GTEKSVTTGN SSGSAPDTVT IASDLATQLN TISGFTVTST DYIIRITKDD GGDYTLESSD TKTADATSAI KG TVDSITD LPTIAEHNFT VRIQGSATTA FDDYFVKFEA TAGSGFGPGV WRETVAPNID HLLDKSTMPH TLVRNANGTF TFA QFNYTG RVAGDTTTAP NPTFVGSKIK NINLFRNRLV FLADENVILS AADSFERFFP ETVQTLLDSD PIDISSGGTS VNFL NSSLA FANTLLLFSL HGQFRLDTGS TSVGTALTPK TATITAITTF DIVDAIDPIG VGRTVYFGIP KGDFSGLREY FLPDA SGPI PLSEEVTSSV PRFVPGNLIS MSPSVSEEVI TMISKDQPRR VYIYKFFFDD DQKLQSSWSY WEVAANKTLL GGNVLD SDL YTCVEYSDGV YLEKTQLRPE TVDSGTEFEI LLDRKTTEAA CSTSLINSGA LGVQTVITLP YPMSGTGTMA VVGRFAS NN TIAHGQVIKA TAETLTGGAS GNGTMTVPGD LSSAKFFVGE IYNMTYEFST PYLKETPPGG GLAVLANPRL QLRTWSIV F DETSNFSMKI TPGQRDELTY PFNGYKIGSG QFPIGTPSLA TGRFRVPVMA QNIETKIVLF SDSPLPCRVQ SAEWEGWYQ ERARRL

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Macromolecule #3: Adaptor protein(gp22) of the cyanophage P-SCSP1u

MacromoleculeName: Adaptor protein(gp22) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)
Molecular weightTheoretical: 22.81148 KDa
SequenceString: MAARTSFLDA VNRVLQMLGE APVNSLQGQF GLAKQAEVAL NDVSRTIQTE GWSFNTDLEK KLERNSSNEI ELSSNVSRVV VDNLEYPDI DVVQRGDKLY DRKNNRYTFD EDLIVDMTTI LEWDLLPEHA RQYITIKAGR QLQEAIIGSA ELTKLNLTQE V EARSAFLE ...String:
MAARTSFLDA VNRVLQMLGE APVNSLQGQF GLAKQAEVAL NDVSRTIQTE GWSFNTDLEK KLERNSSNEI ELSSNVSRVV VDNLEYPDI DVVQRGDKLY DRKNNRYTFD EDLIVDMTTI LEWDLLPEHA RQYITIKAGR QLQEAIIGSA ELTKLNLTQE V EARSAFLE EETTKSEHSM LRGHLNRTSP VNTYIPSRTL ER

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Macromolecule #4: Fiber protein(gp 28) of the cyanophage P-SCSP1u

MacromoleculeName: Fiber protein(gp 28) of the cyanophage P-SCSP1u / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)
Molecular weightTheoretical: 113.856602 KDa
SequenceString: MAFAQRIITS NSAGDQEFTF TFDYIKEEHI KVFVNFVEKA QGTGSNEFQV ITNTTPKKIS LNTGLSADNT RVEIRRVSSL STPLVDFAD GSTLTAADLD TAEKQSLFID QELDDALKQG ISIDTSTGVP TLNSQRLSNV SDPVNAQDAV TKAYLERSGS I TSTQILNG ...String:
MAFAQRIITS NSAGDQEFTF TFDYIKEEHI KVFVNFVEKA QGTGSNEFQV ITNTTPKKIS LNTGLSADNT RVEIRRVSSL STPLVDFAD GSTLTAADLD TAEKQSLFID QELDDALKQG ISIDTSTGVP TLNSQRLSNV SDPVNAQDAV TKAYLERSGS I TSTQILNG TIVDADINAS AAIAKSKLAA LNIVNADVNA SAAIAGSKLA DASIAYTKIQ NVSATNRILG RDSSGAGVIE EI TPANLRT MINVEDGATA DQSAAEIRTL VESASDSNVF TDADHTKLNA IEASADVTDA TNVDAAGAVM NSDTSTAAMQ FVI DEDTFG SNLDTKVPTQ QSVKAYITAT SQPLDSELSQ LAGMQSGTAS KLADSTALTA DIADLNQLDG MAKETSITNS NTKF PTSAA VVNFVANQIA PVGGLEVIAD EDSFPATQPV SGVVISISNA DGLVINNAGE ASNARTVGSG SDNVTIKNFP ASLRN QTLA PNLGLLVSST GASQEYNYHK LLAKETDVLQ LSDDINDFNN RYRVENTLPA ANDSSNHDGD LVYAKEEKKI YVYSGD YNG TPVGSFGEVQ SIGNFFISTL SPAFNGSLQD FTITNAPSNA QQIILSINGV IQKPNSGTST PSEGFALSGS TIKLAAA PP SGADYFAIVL GSTVNIGTPS NNTVTSSILQ NGSVIEAKLG SGAVTRTKLN LVSTSSAPGL EVKGDGSSDG YLQLNCSQ N SHGIKLKSPP HSAGQSYTLT FPSNIVSGQF LTTDANGNLS WAAVVTDLVN DTSPQLGGNL DCNDKNILLN DSSGSANNR IRLGASQDFA LFHNGTINII EAVSGDLHLR LNGSEEGIIV KQNGAVELYY DNSKKFHTSS VGATVTGNLF LSGGYINLND NYSYGMGSG NRAQLYHSGN HQYLLNTVGN MYFQPKSGEN GIVIIPDDAV ELYHNNVKRL ETTSGGVTVS GSVTATGHLF V GANTHYLY FTSTAGYSPR IGNADGGTGV NMTFHTNNTM RMMLQNDGHL RPASNNTYDL GTSSDRWRNV YTNDLNLSNE GG ANDVDGT WGSYTIQEGA EDLFLINKRT SKKYKFNLTE VS

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 86469
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

Initial modelDetails: the initial model of our models was predicted by the alpha fold according to the protein sequence.
Output model

PDB-8i4m:
Portal-tail complex structure of the Cyanophage P-SCSP1u

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