+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31078 | |||||||||
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Title | Cyanophage Pam1 capsid asymmetric unit | |||||||||
Map data | An asymmetric unit of Pam1 capsid.Cutting out using phenix Map box program. | |||||||||
Sample | Pam1 != unidentified Pam1
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Keywords | Major capsid and cement proteins / VIRUS | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 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_31078.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-31078-v30.xml emd-31078.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_31078.png | 160.7 KB | ||
Filedesc metadata | emd-31078.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31078 | HTTPS FTP |
-Validation report
Summary document | emd_31078_validation.pdf.gz | 441.5 KB | Display | EMDB validaton report |
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Full document | emd_31078_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | emd_31078_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_31078_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31078 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31078 | HTTPS FTP |
-Related structure data
Related structure data | 7eelMC 7eeaC 7eepC 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_31078.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | An asymmetric unit of Pam1 capsid.Cutting out using phenix Map box program. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Major capsid proteins
Macromolecule | Name: Major capsid proteins / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 39.379066 KDa |
Sequence | String: MADFSLATAS QRKEWSNKAH MEYVRRSRFA PYIRNTENSI FQGYSDLEKR AGDTLNIPLF YKLGGAPVTG DTPIVGNETP LDNYNCGVP VALRGKGVAI TKNQTFRTEI DVMNAAKQSL TRYFGELLRD DIIEALGSVV TTGDTTVNYG SASAANRNAF S AANPDRLF ...String: MADFSLATAS QRKEWSNKAH MEYVRRSRFA PYIRNTENSI FQGYSDLEKR AGDTLNIPLF YKLGGAPVTG DTPIVGNETP LDNYNCGVP VALRGKGVAI TKNQTFRTEI DVMNAAKQSL TRYFGELLRD DIIEALGSVV TTGDTTVNYG SASAANRNAF S AANPDRLF FGSISGYSAT WATGLGNVDA AETCTAARVG VMKRLAMSAS PAITPMQVDD DEGREYFVAF HGSRTFRDLK GD TAMLNAN REARPRDVSS NPLLQDGDLI YEGVIHREVP EIDAWAAANG FNTAGAGSAP IRPVFLCGTQ SVFLAYAQRP QAG TEKSDI PALNRRMTVG MDEIIGVKKA AFNGKQHGVV MGFFGAAGD |
-Macromolecule #2: Cement (decoration) proteins
Macromolecule | Name: Cement (decoration) proteins / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 13.831203 KDa |
Sequence | String: MPATNSAQAR LAAPGHGFGG NVKVSYGSVA FTGTITTADA ATVCNLPVGA IVLGVTLESD DLDTNATPTI TLNVGDAGSA TRYFSASTV AQAGTSSSAP ATTGLLWTVT EGNTAVRIAV ANNAATSADG SVRVAVTYYL P |
-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 |
-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: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 21210 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |