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Yorodumi- EMDB-43292: Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein V... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43292 | |||||||||
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Title | Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 9-14-18, DTT-treated | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virion capsid / capsid protein / Tulane virus / VIRUS | |||||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Viral coat protein subunit / Capsid protein Function and homology information | |||||||||
Biological species | Tulane virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.63 Å | |||||||||
Authors | Sun C / Jiang W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biomolecules / Year: 2024 Title: The 2.6 Å Structure of a Tulane Virus Variant with Minor Mutations Leading to Receptor Change. Authors: Chen Sun / Pengwei Huang / Xueyong Xu / Frank S Vago / Kunpeng Li / Thomas Klose / Xi Jason Jiang / Wen Jiang / Abstract: Human noroviruses (HuNoVs) are a major cause of acute gastroenteritis, contributing significantly to annual foodborne illness cases. However, studying these viruses has been challenging due to ...Human noroviruses (HuNoVs) are a major cause of acute gastroenteritis, contributing significantly to annual foodborne illness cases. However, studying these viruses has been challenging due to limitations in tissue culture techniques for over four decades. Tulane virus (TV) has emerged as a crucial surrogate for HuNoVs due to its close resemblance in amino acid composition and the availability of a robust cell culture system. Initially isolated from rhesus macaques in 2008, TV represents a novel belonging to the genus. Its significance lies in sharing the same host cell receptor, histo-blood group antigen (HBGA), as HuNoVs. In this study, we introduce, through cryo-electron microscopy (cryo-EM), the structure of a specific TV variant (the 9-6-17 TV) that has notably lost its ability to bind to its receptor, B-type HBGA-a finding confirmed using an enzyme-linked immunosorbent assay (ELISA). These results offer a profound insight into the genetic modifications occurring in TV that are necessary for adaptation to cell culture environments. This research significantly contributes to advancing our understanding of the genetic changes that are pivotal to successful adaptation, shedding light on fundamental aspects of evolution. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43292.map.gz | 232.9 MB | EMDB map data format | |
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Header (meta data) | emd-43292-v30.xml emd-43292.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_43292.png | 239 KB | ||
Masks | emd_43292_msk_1.map emd_43292_msk_2.map | 669.9 MB 669.9 MB | Mask map | |
Filedesc metadata | emd-43292.cif.gz | 5.8 KB | ||
Others | emd_43292_half_map_1.map.gz emd_43292_half_map_2.map.gz | 232.7 MB 232.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43292 | HTTPS FTP |
-Validation report
Summary document | emd_43292_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_43292_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_43292_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_43292_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43292 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43292 | HTTPS FTP |
-Related structure data
Related structure data | 8vjrMC 8vgrC 8vjsC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43292.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.104 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43292_msk_1.map | ||||||||||||
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Density Histograms |
-Mask #2
File | emd_43292_msk_2.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_43292_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43292_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tulane virus
Entire | Name: Tulane virus |
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Components |
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-Supramolecule #1: Tulane virus
Supramolecule | Name: Tulane virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: The Tulane virus was purified from the LLC-MK2 cell line. NCBI-ID: 512169 / Sci species name: Tulane virus / Sci species strain: 9-6-17 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 57 MDa |
Virus shell | Shell ID: 1 / Diameter: 400.0 Å |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Tulane virus |
Molecular weight | Theoretical: 57.933172 KDa |
Sequence | String: MESSKTEQVT GATGITQSTV TAPLPEAVSS LSLAPTVNAL DPWVYLNQTE VPGGTFTVSS ATQPGSVLLE LEISPELNLY TSHLFRMYA GWSGGFSLKL LVAGNAFSAG KLIAAIIPPN IEVPNSAYLL TGFPHEILDF RTADSMEIIA PDIKNIDYHF R GDKLGKLV ...String: MESSKTEQVT GATGITQSTV TAPLPEAVSS LSLAPTVNAL DPWVYLNQTE VPGGTFTVSS ATQPGSVLLE LEISPELNLY TSHLFRMYA GWSGGFSLKL LVAGNAFSAG KLIAAIIPPN IEVPNSAYLL TGFPHEILDF RTADSMEIIA PDIKNIDYHF R GDKLGKLV VMVYSPLRST SADFEIEIKL TSAPLPDFKF TMLVPPIQNN ALPIWSIPQA PPYSMVNPRS PLTPVVELYI NS SYATCNH QLGRYTIYQG AIGNSTFNPS GAWTATCTAE AGSVTGHPNW RYALLDLPDN PTFDPTLPPV PRGFCDWGSG VKS GNKQHL VCFTGKKVEG GFQDVDTHMW DYGDNETVGL DNTYQRTIYI KDPSLEKDAQ YLVIPMGVSG AANDDTVQVA PNCY GSWDY APTVAPPLGE QFVWFRSQLP ASKTTTTSGV NSVPVNVNAL MSPDLMCSAY ASGFPLGKVA LLDYVLFGGS VVRQF KLYP EGYMTANTTG SNTGFIIPAD GYFRFNSWVS PSFMISSVVD LNLQTAVVFR UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: GATAN CRYOPLUNGE 3 |
Details | Purified virus |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 969 / Average electron dose: 23.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 44239 |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC / Details: Cryosparc ab-initial reconstruction |
Final angle assignment | Type: OTHER / Software: (Name: cryoSPARC, jspr) |