+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18445 | |||||||||
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Title | Neck of phage 812 virion (C12) | |||||||||
Map data | Neck of phage 812 virion (C12) | |||||||||
Sample |
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Keywords | phage / neck / portal / connector / VIRUS | |||||||||
Function / homology | Bacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont entry into host cell / Portal protein / Neck protein Function and homology information | |||||||||
Biological species | Staphylococcus phage 812 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.16 Å | |||||||||
Authors | Cienikova Z / Novacek J / Fuzik T / Benesik M / 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_18445.map.gz | 29.3 MB | EMDB map data format | |
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Header (meta data) | emd-18445-v30.xml emd-18445.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18445_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_18445.png | 70.4 KB | ||
Masks | emd_18445_msk_1.map | 274.6 MB | Mask map | |
Filedesc metadata | emd-18445.cif.gz | 6.7 KB | ||
Others | emd_18445_half_map_1.map.gz emd_18445_half_map_2.map.gz | 209.6 MB 209.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18445 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18445 | HTTPS FTP |
-Validation report
Summary document | emd_18445_validation.pdf.gz | 823.8 KB | Display | EMDB validaton report |
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Full document | emd_18445_full_validation.pdf.gz | 823.3 KB | Display | |
Data in XML | emd_18445_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_18445_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18445 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18445 | HTTPS FTP |
-Related structure data
Related structure data | 8qjeMC 8q01C 8q1iC 8q7dC 8qekC 8qemC 8qgrC 8qkhC C: citing same article (ref.) M: atomic model generated by this map |
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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_18445.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Neck of phage 812 virion (C12) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18445_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_18445_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_18445_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
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: #1-#2 / Details: Purified phage virion / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K1-420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Staphylococcus aureus (bacteria) / Strain: CCM 8428 |
Virus shell | Shell ID: 1 / Diameter: 1100.0 Å |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage 812 (virus) / Strain: K1-420 |
Molecular weight | Theoretical: 64.155684 KDa |
Sequence | String: MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLK KFGNNPILNA IILTRSNQVA MYCQPARYSE KGLGFEVRLR DLDAEPGRKE KEEMKRIEDF IVNTGKDKDV D RDSFQTFC ...String: MADLFKQFRL GKDYGNNSTI AQVPIDEGLQ ANIKKIEQDN KEYQDLTKSL YGQQQAYAEP FIEMMDTNPE FRDKRSYMKN EHNLHDVLK KFGNNPILNA IILTRSNQVA MYCQPARYSE KGLGFEVRLR DLDAEPGRKE KEEMKRIEDF IVNTGKDKDV D RDSFQTFC KKIVRDTYIY DQVNFEKVFN KNNKTKLEKF IAVDPSTIFY ATDKKGKIIK GGKRFVQVVD KRVVASFTSR EL AMGIRNP RTELSSSGYG LSEVEIAMKE FIAYNNTESF NDRFFSHGGT TRGILQIRSD QQQSQHALEN FKREWKSSLS GIN GSWQIP VVMADDIKFV NMTPTANDMQ FEKWLNYLIN IISALYGIDP AEIGFPNRGG ATGSKGGSTL NEADPGKKQQ QSQN KGLQP LLRFIEDLVN RHIISEYGDK YTFQFVGGDT KSATDKLNIL KLETQIFKTV NEAREEQGKK PIEGGDIILD ASFLQ GTAQ LQQDKQYNDG KQKERLQMMM SLLEGDNDDS EEGQSTDSSN DDKEIGTDAQ IKGDDNVYRT QTSNKGQGRK GEKSSD FKH UniProtKB: Portal protein |
-Macromolecule #2: Putative neck protein
Macromolecule | Name: Putative neck 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: 34.191703 KDa |
Sequence | String: MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERA LDISILPDTQ HEMRDYHETE FNSYMFVHAY RKPILQVENL QLQFNGRPIY KYPANWWKVE HLAGHVQLFP T ALMQTGQS ...String: MVNSMFGGDL DPYEKSLNYE YPYHPSGNPK HIDVSEIDNL TLADYGWSPD AVKAYMFGIV VQNPDTGQPM GDEFYNHILE RAVGKAERA LDISILPDTQ HEMRDYHETE FNSYMFVHAY RKPILQVENL QLQFNGRPIY KYPANWWKVE HLAGHVQLFP T ALMQTGQS MSYDAVFNGY PQLAGVYPPS GATFAPQMIR LEYVSGMLPR KKAGRNKPWE MPPELEQLVI KYALKEIYQV WG NLIIGAG IANKTLEVDG ITETIGTTQS AMYGGASAQI LQINEDIKEL LDGLRAYFGY NMIGL UniProtKB: Neck protein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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 / 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 30553 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000 |
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 |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: cross-correlation coefficient | ||||||
Output model | PDB-8qje: |