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- EMDB-45962: Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein V... -

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Basic information

Entry
Database: EMDB / ID: EMD-45962
TitleCryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 5-12-18
Map data
Sample
  • Virus: Tulane virus
    • Protein or peptide: Capsid protein
KeywordsTulane virus / capsid protein / VIRUS
Function / homologyCalicivirus 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 speciesTulane virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSun C / Jiang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI111095 United States
CitationJournal: 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
DepositionJul 29, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45962.png

Downloads & links

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Map

FileDownload / File: emd_45962.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 480 pix.
= 622.8 Å		1.3 Å/pix.
x 480 pix.
= 622.8 Å		1.3 Å/pix.
x 480 pix.
= 622.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.129
Minimum - Maximum-0.4080002 - 0.56785643
Average (Standard dev.)-0.0026950173 (±0.041945882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 622.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45962_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45962_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Tulane virus

EntireName: Tulane virus
Components
  • Virus: Tulane virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Tulane virus

SupramoleculeName: Tulane virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 512169 / Sci species name: Tulane virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 57 MDa

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tulane virus
Molecular weightTheoretical: 57.933172 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 23.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.0) / Number images used: 10827
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.0.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8vg6
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9cve:
Cryo-EM structure of Tulane virus 9-6-17 variant capsid protein VP1 5-12-18

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