+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18065 | |||||||||
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Title | Neck-tail junction of phage 812 after tail contraction (C6) | |||||||||
Map data | Neck-tail junction of phage 812 after tail contraction (C6) | |||||||||
Sample |
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Keywords | phage / neck / connector / tail sheath / VIRUS | |||||||||
Function / homology | Major tail sheath protein / Baseplate hub assembly protein Function and homology information | |||||||||
Biological species | Staphylococcus phage 812 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||
Authors | Cienikova Z / Siborova M / Fuzik T / Plevka P | |||||||||
Funding support | Czech Republic, 1 items
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Citation | Journal: To Be Published Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812 Authors: Cienikova Z / Novacek J / Siborova M / Popelarova B / Fuzik T / Benesik M / Bardy P / Plevka P | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18065.map.gz | 54.1 MB | EMDB map data format | |
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Header (meta data) | emd-18065-v30.xml emd-18065.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18065_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_18065.png | 88.6 KB | ||
Masks | emd_18065_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-18065.cif.gz | 6.7 KB | ||
Others | emd_18065_half_map_1.map.gz emd_18065_half_map_2.map.gz | 169.1 MB 168.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18065 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18065 | HTTPS FTP |
-Validation report
Summary document | emd_18065_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_18065_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_18065_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_18065_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18065 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18065 | HTTPS FTP |
-Related structure data
Related structure data | 8q1iMC 8q01C 8q7dC 8qekC 8qemC 8qgrC 8qjeC 8qkhC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18065.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Neck-tail junction of phage 812 after tail contraction (C6) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18065_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1 for neck-tail junction of phage...
File | emd_18065_half_map_1.map | ||||||||||||
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Annotation | Half map 1 for neck-tail junction of phage 812 after tail contraction (C6) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for neck-tail junction of phage...
File | emd_18065_half_map_2.map | ||||||||||||
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Annotation | Half map 2 for neck-tail junction of phage 812 after tail contraction (C6) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Staphylococcus phage 812
Entire | Name: Staphylococcus phage 812 (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage 812
Supramolecule | Name: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K1-420 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428 |
-Macromolecule #1: Tail sheath protein
Macromolecule | Name: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage 812 (virus) / Strain: K1-420 |
Molecular weight | Theoretical: 64.559008 KDa |
Sequence | String: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS ...String: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS VEHDEETQKA SRLVLKVGDQ EVKSYDLTGG AYDYTNAIIT DINQLPDFEA KLSPFGDKNL ESSKLDKIEN AN IKDKAVY VKAVFGDLEK QTAYNGIVSF EQLNAEGEVP SNVEVEAGEE SATVTATSPI KTIEPFELTK LKGGTNGEPP ATW ADKLDK FAHEGGYYIV PLSSKQSVHA EVASFVKERS DAGEPMRAIV GGGFNESKEQ LFGRQASLSN PRVSLVANSG TFVM DDGRK NHVPAYMVAV ALGGLASGLE IGESITFKPL RVSSLDQIYE SIDLDELNEN GIISIEFVRN RTNTFFRIVD DVTTF NDKS DPVKAEMAVG EANDFLVSEL KVQLEDQFIG TRTINTSASI IKDFIQSYLG RKKRDNEIQD FPAEDVQVIV EGNEAR ISM TVYPIRSFKK ISVSLVYKQQ TLQA UniProtKB: Major tail sheath protein |
-Macromolecule #2: Tail terminator protein
Macromolecule | Name: Tail terminator protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage 812 (virus) / Strain: K1-420 |
Molecular weight | Theoretical: 31.79968 KDa |
Sequence | String: MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE ...String: MAITSVDSYL LSEIKPRLNT VLENCYIIDE VLKDFDYQTR ESFKEAFCGK NAQHEVTVGF NFPKFKNNYE AHYLIQLGQG QETKNSLGS IQSSYFEATG DTLVESSTAI REDDKLVFTV SKPIGELIKV EDIEFAKYDN LQVEGNKVSF KYQTNEDYEN Y NANIIFTE KKNDSKGLVK GFTVEEQVTV VGLSFNVDVA RCLDAVLKMI LISMRDSIEE QQTFQLQNLS FGDIAPIIED GD SMIFGRP TIIKYTSSLD LDYTITQDIN KLTFKERKDW K UniProtKB: Baseplate hub assembly protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Phage particle after tail contraction and genome ejection |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 15371 / Average exposure time: 7.0 sec. / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient |
Output model | PDB-8q1i: |