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- EMDB-33802: Cyanophage Pam3 baseplate proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-33802
TitleCyanophage Pam3 baseplate proteins
Map data
Sample
  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Pam3 baseplate wedge gp22
    • Protein or peptide: Pam3 baseplate wedge gp23
    • Protein or peptide: Pam3 sheath initiator gp21
    • Protein or peptide: Pam3 tube initiator gp17
    • Protein or peptide: Pam3 plug gp18
    • Protein or peptide: Pam3 hub gp19
    • Protein or peptide: Pam3 spike gp20
Keywordsbaseplate / VIRUS / VIRAL PROTEIN
Biological speciesuncultured cyanophage (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsYang F / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Fine structure and assembly pattern of a minimal myophage Pam3.
Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
History
DepositionJul 9, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33802.png

Downloads & links

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Map

FileDownload / File: emd_33802.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.02305705 - 0.05986155
Average (Standard dev.)0.00018664611 (±0.002715909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 513.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33802_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33802_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : uncultured cyanophage

EntireName: uncultured cyanophage (environmental samples)
Components
  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Pam3 baseplate wedge gp22
    • Protein or peptide: Pam3 baseplate wedge gp23
    • Protein or peptide: Pam3 sheath initiator gp21
    • Protein or peptide: Pam3 tube initiator gp17
    • Protein or peptide: Pam3 plug gp18
    • Protein or peptide: Pam3 hub gp19
    • Protein or peptide: Pam3 spike gp20

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Supramolecule #1: uncultured cyanophage

SupramoleculeName: uncultured cyanophage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 215796 / Sci species name: uncultured cyanophage / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudanabaena mucicola (bacteria)

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Macromolecule #1: Pam3 baseplate wedge gp22

MacromoleculeName: Pam3 baseplate wedge gp22 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 32.686787 KDa
SequenceString: MTYGVQPTGY VKKPLAVHLA EIEASMVDLF GPGVIQTEQS PLGQLNGLYA DLSYDLDERG EDLYQSFDPE QAEGSRLDIL ARYRLLSRR AGESDESFRR AITNVDRARI DLSDLSTALS AINGVSWSRV YVNEDATTDA DGIPPNTVSV AVIGGDDDEV A QLVRRYVV ...String:
MTYGVQPTGY VKKPLAVHLA EIEASMVDLF GPGVIQTEQS PLGQLNGLYA DLSYDLDERG EDLYQSFDPE QAEGSRLDIL ARYRLLSRR AGESDESFRR AITNVDRARI DLSDLSTALS AINGVSWSRV YVNEDATTDA DGIPPNTVSV AVIGGDDDEV A QLVRRYVV PGVGMYGNTT IETTIGGFCR RIRVIRPVLI PTSVEIDVQS RPLKNGCPPP SVNAMAAGLY TELTGPDRPG NG EDGTVYL FRKIMERLYP NVEVVDVRLS QAPAAPTTPP LVMSFFQMMS FNADDILVEI VP

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Macromolecule #2: Pam3 baseplate wedge gp23

MacromoleculeName: Pam3 baseplate wedge gp23 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 26.194811 KDa
SequenceString: MSNLCADPEA LVEARIDEVL TQYRESPYLL NLIRAYLSKL AETSMSYCDM VEKFDLDTAV GDQLTIIGRI LGFPRCHCVC DTIPVVGYD CGGSYAGSYQ LAGYCEPGSS WIHCSPYGNS ELCVDEDEIY RSLLKARRYQ MLGLYDIESL HEALQIVWGE D AMVAETKV ...String:
MSNLCADPEA LVEARIDEVL TQYRESPYLL NLIRAYLSKL AETSMSYCDM VEKFDLDTAV GDQLTIIGRI LGFPRCHCVC DTIPVVGYD CGGSYAGSYQ LAGYCEPGSS WIHCSPYGNS ELCVDEDEIY RSLLKARRYQ MLGLYDIESL HEALQIVWGE D AMVAETKV GQVVVTPGRS LTATETRYLP IVFRALPIAP GIKGMIHIDQ GPIAGYGDGW AGYCGGDWLC PVDPHAYTCS

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Macromolecule #3: Pam3 sheath initiator gp21

MacromoleculeName: Pam3 sheath initiator gp21 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 13.889669 KDa
SequenceString:
MAAPSRIGLA LKKNEQGIAD IYLDASGNLS MVQNTEAVGQ HARQRLMTYL GEWFLNKNVG VPWLRDLLGK GYDPVLAEAV IKAEILSTD GVTEITSFSI RFDQGRRALE AFDIEVTTEY DEETVL

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Macromolecule #4: Pam3 tube initiator gp17

MacromoleculeName: Pam3 tube initiator gp17 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 19.854342 KDa
SequenceString:
MIIAFSSAIG PVPLTVVISE KHTSKVELTT NPIESGADVT DHAYVKGKEI ELEVADRNAA ATWAALVAFQ ESRVPFVLMT GLSMYRNMI ITEIDATRNA QHSKILKGTV RLREVKIVET GTAEDSSGKD GTDKNKSSNP SKDKAADAKT ADKANSGVNA G DKGGTTVA APRAQSLLKG VFGGSSASGG AAP

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Macromolecule #5: Pam3 plug gp18

MacromoleculeName: Pam3 plug gp18 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 11.724286 KDa
SequenceString:
MIELEVLDES KQKFSVILND RRVTIELWYN TTNDRWSFSL ALDGDNVVTG RRLVTGVDLL APFGLGIGAL FLLSENGEPP TRANLPLGL VKLYHATQEE IDAAISA

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Macromolecule #6: Pam3 hub gp19

MacromoleculeName: Pam3 hub gp19 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 25.201736 KDa
SequenceString: MLEVGYTPPG GGNNIGIIAK GKIRDYQHDR EGGDIISTVS CGDGDKAYRR ATISKTIPKG TPLTEVVDEI HKEMKKEGIA KGEWSFPDK VKNTQLKRPY SMCGSCTREL DTLGRSHGFY WNIQNETMEI IPGNGHLPGS LLITPDTGLI GTPTITDNGI K VKALINPE ...String:
MLEVGYTPPG GGNNIGIIAK GKIRDYQHDR EGGDIISTVS CGDGDKAYRR ATISKTIPKG TPLTEVVDEI HKEMKKEGIA KGEWSFPDK VKNTQLKRPY SMCGSCTREL DTLGRSHGFY WNIQNETMEI IPGNGHLPGS LLITPDTGLI GTPTITDNGI K VKALINPE ARPNRMMKVK SQVLKMNRKG EDYRISEVSF NGDNQEGDWI MTLTGEAIGG DKKVDEGKKA K

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Macromolecule #7: Pam3 spike gp20

MacromoleculeName: Pam3 spike gp20 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 23.537537 KDa
SequenceString: MTGYLGKTTN QDRDVVSAVA QSERESVWGE MPGRVVSVSA DGRTVTVQPL YKPKFNGVPT DMPVLQEVPL RQALMGGVGV TVPVKPGQN VTLRPQMRSM DNYHVEGDGS ASDSRSFSLS DMEAHIAGGE SLKDVIPNLD SENVHVRANA DGSKGMKLSP E GKVEFQGP ...String:
MTGYLGKTTN QDRDVVSAVA QSERESVWGE MPGRVVSVSA DGRTVTVQPL YKPKFNGVPT DMPVLQEVPL RQALMGGVGV TVPVKPGQN VTLRPQMRSM DNYHVEGDGS ASDSRSFSLS DMEAHIAGGE SLKDVIPNLD SENVHVRANA DGSKGMKLSP E GKVEFQGP EGNLLDLIAD FMELVANDKL QINYGSSAGT NHAMANKAAM LALAAKVRTT GTI

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 45155
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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