+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22896 | |||||||||
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Title | The Neck region of Phage XM1 (6-fold symmetry) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Myoviridae / Phage / 6-fold neck region / VIRAL PROTEIN | |||||||||
Biological species | Vibrio phage XM1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang Z / Klose T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biorxiv / Year: 2021 Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine Authors: Wang Z / Fokine A / Guo X / Jiang W / Rossmann MG / Kuhn RJ / Luo ZH / Klose T | |||||||||
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_22896.map.gz | 51.4 MB | EMDB map data format | |
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Header (meta data) | emd-22896-v30.xml emd-22896.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22896_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_22896.png | 142.6 KB | ||
Filedesc metadata | emd-22896.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22896 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22896 | HTTPS FTP |
-Validation report
Summary document | emd_22896_validation.pdf.gz | 500.1 KB | Display | EMDB validaton report |
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Full document | emd_22896_full_validation.pdf.gz | 499.6 KB | Display | |
Data in XML | emd_22896_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_22896_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22896 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22896 | HTTPS FTP |
-Related structure data
Related structure data | 7kjkMC 7kh1C 7klnC 7kmxC 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_22896.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.81 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 : Vibrio phage XM1
Entire | Name: Vibrio phage XM1 (virus) |
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Components |
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-Supramolecule #1: Vibrio phage XM1
Supramolecule | Name: Vibrio phage XM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2748688 / Sci species name: Vibrio phage XM1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Vibrio rotiferianus (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Tail terminator protein
Macromolecule | Name: Tail terminator protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 18.236037 KDa |
Sequence | String: MSQSIINVAR YIRDLLDYDE NLIQFDRKNT QQSDTVTGYI VVNGSGVQNV LSHGSSYDGD AEIMEYSKSE SRLITLEFYG SDAYENAEL FSLLNQSQKA KEVSRGLGLT IYNVSQATDV KQLLGYQYGN RVHVDFNIQY CPSVYVETLR VDASEFEILV D D |
-Macromolecule #2: Collar spike protein
Macromolecule | Name: Collar spike protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 90.692562 KDa |
Sequence | String: MSIQVTGIIE GPLGTPSPGI TIRVVSKISY RNTYRLSTED YVTTTGGAYD FQLNEGFHKI LIRYRGASSF TKLGDVSVSD QTPSPITLI NLLESSSPKA LVVKLQELAD EASESAQSAS DDADQVTLDK QQVTLLAQQV SDDADQVALD RSATAQSEVN A AQSATTAQ ...String: MSIQVTGIIE GPLGTPSPGI TIRVVSKISY RNTYRLSTED YVTTTGGAYD FQLNEGFHKI LIRYRGASSF TKLGDVSVSD QTPSPITLI NLLESSSPKA LVVKLQELAD EASESAQSAS DDADQVTLDK QQVTLLAQQV SDDADQVALD RSATAQSEVN A AQSATTAQ QSADDAAAIV PNLQSQIDDK IDKTQSIIPD VDALFSLGRH EINPTNNNIP GLSGTRSLLH IQNNLGGFQL AA RTVGSEI HVRSADTNSG NIGPWERLYT TGYRPSSYDL VVKDKAEALS VSHQEGLIIG IESCNGARFV SVLPSDSGGL YLG SLPNGN KLRHIPLDGF SLKTIRTSDF EINSGSDVSQ FLIDASTAGY GQVYIDNDCE VTQLCDITGV KYLESLNGAE MLID DLNGR VKCDTDGFEV KGIVFKKSGD YSNTTFEAYL LETNGEKSLA SRCQFVGQWA GYKLQGNDSS ADLCFFSDGT FMLRV GEGV SSCNINRCFF TRGTRRFTEG EQQGDGIKLT AQSSTQGYNE NIIISDCIFY DTYRDCIDGY VGANRLIVKG SIMLNW GAH ALDFKSRVDD NSESPDGGPL TRNVLVDGCM IWKDVVRPDF DLTLAAVVMS VIPGALPVPT SEADVRQNGL RGMELKN TL IAYKGNGSLI SAASTWRTVI DGCTLTDLGQ IGQIIYAPNS WHLKLINSTV NIDPSNINNV KFSSAMNNAE VNDNTFNR L LISTDGMIRT SIKRNKFNGE GVLSRGLNIA SEEVSAVSNE FENFTSFGAQ IFNSASKCRF DFNEIRNCPA PLGIENPSV NTYHSVRGNI SMGSGAFTGL NRITDNGGVA NGNDHVPYS |
-Macromolecule #3: Head completion protein
Macromolecule | Name: Head completion protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 13.045932 KDa |
Sequence | String: MLPNMRSALK MFEQSVLLKS VETIRVDFVD DIIITATPIR AVVQVADKKK LNLDSLDWSK QYIWVHSGSK MEIGQFIEWH GKDFKLVAA GDDYSDYGYN AWYGEETLKP VLVSS |
-Macromolecule #4: Tail tube protein
Macromolecule | Name: Tail tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 15.665332 KDa |
Sequence | String: MSVIVYRNNQ STLTLNGYTF QHLYQGAALV LTPVNAKTAR TNSINGGVSI SGRVDGGVHT LAIMVQKHSP DDKFLNDAKN SQEPVVFDG SMKRAYTESG TLKKATTTLE TGSITTQPTK TDNNQDPDDS RTYVIEFRNS VETF |
-Macromolecule #5: Tail sheath protein
Macromolecule | Name: Tail sheath protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 53.006762 KDa |
Sequence | String: MASISEVIRV SLQQEGRAIA PDNMNAVGII TGNQGVLSTA DRYRIYRTAA AVASDFGASS QESAFANTFF DTTPNPISAG GVLVIGYWR SASETVAATS ATLVSEQTSE SVLIPLLNAI NDGSFTITVD GGTEQEVTAL DFTGVSELSE VATILNSAIT G ATVSEDNG ...String: MASISEVIRV SLQQEGRAIA PDNMNAVGII TGNQGVLSTA DRYRIYRTAA AVASDFGASS QESAFANTFF DTTPNPISAG GVLVIGYWR SASETVAATS ATLVSEQTSE SVLIPLLNAI NDGSFTITVD GGTEQEVTAL DFTGVSELSE VATILNSAIT G ATVSEDNG YFKVTSSTTG ATSLLSYLGV ATSGTDISAV LGMNSESGAV LTQGTDQVVL PAETKLEGIT AIKSEVNIKG AM FIDQILD ADIPGIASFA GANNMLVYEV FDTGYLSKNV SNPVWAVKLA GQSNFRCLLS KSGNRKFAAT YMARMHTVLF SGQ NTAITM QLKELSVTAE EYTDTEIANA KTVGLDLLTT IKNEQALLTS GANDFCDNVY NLEAFRDEIQ TNNYNLLKTT STKI PQTDP GMDTIEDDTE KTCEKYVRNG VFAPGTWTRS DFFGDRQQFV DAIAQKGYYV LIGDLADQTT AERQSRVSPV IQIAV KNAG AVHEEDIIIS VNL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4 |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |