+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31079 | |||||||||
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Title | Cyanophage Pam1 portal-adaptor complex | |||||||||
Map data | ||||||||||
Sample | Pam1 != unidentified Pam1
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Keywords | Portal and adaptor proteins / VIRUS | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Zhang JT / Jiang YL | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31079.map.gz | 95.9 MB | EMDB map data format | |
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Header (meta data) | emd-31079-v30.xml emd-31079.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_31079.png | 102.1 KB | ||
Filedesc metadata | emd-31079.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31079 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31079 | HTTPS FTP |
-Validation report
Summary document | emd_31079_validation.pdf.gz | 662.3 KB | Display | EMDB validaton report |
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Full document | emd_31079_full_validation.pdf.gz | 661.8 KB | Display | |
Data in XML | emd_31079_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_31079_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31079 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31079 | HTTPS FTP |
-Related structure data
Related structure data | 7eepMC 7eeaC 7eelC 7eeqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31079.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.013 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pam1
Entire | Name: Pam1 |
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Components |
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-Supramolecule #1: unidentified
Supramolecule | Name: 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 |
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Host (natural) | Organism: Pseudanabaena mucicola (bacteria) |
-Macromolecule #1: Pam1 portal proteins
Macromolecule | Name: Pam1 portal proteins / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 67.483438 KDa |
Sequence | String: 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 |
-Macromolecule #2: Pam1 adaptor proteins
Macromolecule | Name: Pam1 adaptor proteins / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 19.901504 KDa |
Sequence | String: MITCRDIITL GLQQARVVPL GREPKAKEAD AGLTVLQSIY DSMFADGPLG PFTEVYATSA YTAQENERIV TNGAAITIPQ TITEGNETR KPYDLTAIIV INGAAQENHV FSLGRWQTAH DLTLNSEAPL AERDKAGLAA LFAMEFAEMF GAELPPRTTA R GFRFKGAI SQKLATKRDD PVYY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.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 assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |