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- EMDB-31079: Cyanophage Pam1 portal-adaptor complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31079
TitleCyanophage Pam1 portal-adaptor complex
Map data
SamplePam1 != unidentified

Pam1

  • Virus: unidentified (others)
    • Protein or peptide: Pam1 portal proteins
    • Protein or peptide: Pam1 adaptor proteins
KeywordsPortal and adaptor proteins / VIRUS
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsZhang JT / Jiang YL
Funding support China, 1 items
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, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0166
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0166
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eep
  • Surface level: 0.0166
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31079.png

Downloads & links

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Map

FileDownload / File: emd_31079.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.013 Å
Density
Contour LevelBy AUTHOR: 0.0166 / Movie #1: 0.0166
Minimum - Maximum-0.052478887 - 0.08059533
Average (Standard dev.)0.00023772575 (±0.004628863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0131.0131.013
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z303.900303.900303.900
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0520.0810.000

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Supplemental data

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Sample components

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Entire : Pam1

EntireName: Pam1
Components
  • Virus: unidentified (others)
    • Protein or peptide: Pam1 portal proteins
    • Protein or peptide: Pam1 adaptor proteins

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Supramolecule #1: unidentified

SupramoleculeName: unidentified / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 32644 / Sci species name: unidentified / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudanabaena mucicola (bacteria)

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Macromolecule #1: Pam1 portal proteins

MacromoleculeName: Pam1 portal proteins / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 67.483438 KDa
SequenceString: MEDTMTMPSH AQLKAYFEEA RDANEEYRKE AFIDRDYFDG HQWTEEELQK LEARKQPATY FNEVKLSIRG LVGVFEQGDS DPRAWPRNP QDEDSADIAT KALRYVKDYS EWSDERSRAA LNYFVEGTCA AIVGVDENGR PEIEPIRFEE FFHDPRSREL D FSDARFKG ...String:
MEDTMTMPSH AQLKAYFEEA RDANEEYRKE AFIDRDYFDG HQWTEEELQK LEARKQPATY FNEVKLSIRG LVGVFEQGDS DPRAWPRNP QDEDSADIAT KALRYVKDYS EWSDERSRAA LNYFVEGTCA AIVGVDENGR PEIEPIRFEE FFHDPRSREL D FSDARFKG VAKWRFADEV GMEYGIKGEI DGALDGDSEG LSIGGDTFGD RPDGKISSWI DSKLRRVFVV EMYVRWNGVW IR ALFWGRG ILEMSVSAYL DRNGKPTCPI EARSCYIDRE NRRYGEVRDL RSPQDAINKR ESKLLHMLNN RQAIATNPEY AYN SDAEMV RKEMSKPDGI IPPGWQPASM TDLANGQFAL LSSAREFIQR IGQNPSVLAA QSASASGRAQ LARQQAGMVD SAMA LNGLR RFELAVYRQA WLRCRQFWKA PDYIRVTDDE GAPQFVGINQ PIKGPPQPVL NEMGQVVIAE PILGYENALA ELDVD INID AVPDTANLAQ EQFLQLTELA RLYGPQEVPF DDLLELSSMP EKTKLIAKRR ERSEQMAQVQ AQQGQMQEQI AMQGAM AEI ENTQADTAYL AARAQNEMLK PQIEAFKAGF GAA

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Macromolecule #2: Pam1 adaptor proteins

MacromoleculeName: Pam1 adaptor proteins / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 19.901504 KDa
SequenceString:
MITCRDIITL GLQQARVVPL GREPKAKEAD AGLTVLQSIY DSMFADGPLG PFTEVYATSA YTAQENERIV TNGAAITIPQ TITEGNETR KPYDLTAIIV INGAAQENHV FSLGRWQTAH DLTLNSEAPL AERDKAGLAA LFAMEFAEMF GAELPPRTTA R GFRFKGAI SQKLATKRDD PVYY

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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
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: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 21762
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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