[English] 日本語
![](img/lk-miru.gif)
- EMDB-43292: Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein V... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 9-14-18, DTT-treated | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | virion capsid / ![]() ![]() ![]() | |||||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sun C / Jiang W | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 232.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 239 KB | ||
Masks | ![]() ![]() | 669.9 MB 669.9 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 232.7 MB 232.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vjrMC ![]() 8vgrC ![]() 8vjsC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.104 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Mask #2
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_43292_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_43292_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Tulane virus
Entire | Name: ![]() ![]() |
---|---|
Components |
|
-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 |
---|---|
Host (natural) | Organism: ![]() ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 / Details: PBS |
---|---|
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 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC / Details: Cryosparc ab-initial reconstruction |
Final angle assignment | Type: OTHER / Software: (Name: cryoSPARC, jspr) |
Final reconstruction | Applied symmetry - Point group: I (icosahedral![]() |