+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31080 | |||||||||
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Title | Cyanophage Pam1 tail machine | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Needle head proteins and tailspike head-binding proteins / VIRAL PROTEIN | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.96 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_31080.map.gz | 165.7 MB | EMDB map data format | |
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Header (meta data) | emd-31080-v30.xml emd-31080.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_31080.png | 161.9 KB | ||
Filedesc metadata | emd-31080.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31080 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31080 | HTTPS FTP |
-Validation report
Summary document | emd_31080_validation.pdf.gz | 669.7 KB | Display | EMDB validaton report |
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Full document | emd_31080_full_validation.pdf.gz | 669.3 KB | Display | |
Data in XML | emd_31080_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_31080_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31080 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31080 | HTTPS FTP |
-Related structure data
Related structure data | 7eeqMC 7eeaC 7eelC 7eepC 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_31080.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Pam1
Supramolecule | Name: Pam1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: unidentified (others) |
-Macromolecule #1: Needle head proteins
Macromolecule | Name: Needle head proteins / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 48.534621 KDa |
Sequence | String: MKIPYGLGAY TRNRGNLPPL ELINLFVEKS DSQGVILQSR KALVEVADVG AGPVRATFQK DGVFGGDRFT LSGDEFYRGA TLLGTVAGG GQARIVSNGL EVLVNAGGLV YSYNGTNFIN AGFPEAAATT IAFTGRYFIG LSAGTGEWYF SAVNNGRSWD A LDFATAEN ...String: MKIPYGLGAY TRNRGNLPPL ELINLFVEKS DSQGVILQSR KALVEVADVG AGPVRATFQK DGVFGGDRFT LSGDEFYRGA TLLGTVAGG GQARIVSNGL EVLVNAGGLV YSYNGTNFIN AGFPEAAATT IAFTGRYFIG LSAGTGEWYF SAVNNGRSWD A LDFATAEN EPDALLDVLV LDGVLVFFGT ESIEFWGFTG DADLPYSPIQ QRVFEQGIYA TGCAVRVDNS FYWVGKDKIV YR NGDVPQA VSDDGIVEKA EGSTNLTLFV LEDERHKFVC LRGDDFTHPH DVTTGQWCEF KSYGRTNFRA TADFGDDETG KIW AWGGYD DEGIIERLFM AGAALEEATQ IDNIRLTCEV GTTPNLVGIY TDPTLEMRFS YDAGNTWEDW EAETLGAQGK YRQR VEWRA LGMFDDPGAL FQFRITDPVS FRLSDVQANA ATGGRQR |
-Macromolecule #2: Tailspike head-binding domain
Macromolecule | Name: Tailspike head-binding domain / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 10.782913 KDa |
Sequence | String: MAAELHITPS RATSSNGLNL DGAKWFFYQT GTTTPQSVYT TAALSVAHSN PVVADAAGKF PAIYFDTTLE YRGVLKTADE ATTIYDIDP INSGILSVLG TSS |
-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 |