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- EMDB-52037: Structure of Tulane virus -

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Basic information

Entry
Database: EMDB / ID: EMD-52037
TitleStructure of Tulane virus
Map data
Sample
  • Virus: Tulane virus
    • Protein or peptide: Capsid protein
KeywordsCapsid / Tulane Virus / Calicivirus / VIRUS
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Viral coat protein subunit / host cell cytoplasm / Capsid protein
Function and homology information
Biological speciesTulane virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsBhella D / Conley MJ
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T002239/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00034/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17135 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X011879/1 United Kingdom
CitationJournal: Viruses / Year: 2024
Title: Conformational Flexibility in Capsids Encoded by the .
Authors: Charlotte B Lewis / Lee Sherry / Michaela J Conley / Masaaki Nakashima / Shirin Akbar / Nithya Govindan / Margaret J Hosie / David Bhella /
Abstract: Caliciviruses are a diverse group of non-enveloped, positive-sense RNA viruses with a wide range of hosts and transmission routes. Norovirus is the most well-known member of the ; the acute ...Caliciviruses are a diverse group of non-enveloped, positive-sense RNA viruses with a wide range of hosts and transmission routes. Norovirus is the most well-known member of the ; the acute gastroenteritis caused by human norovirus (HuNoV), for example, frequently results in closures of hospital wards and schools during the winter months. One area of calicivirus biology that has gained increasing attention over the past decade is the conformational flexibility exhibited by the protruding (P) domains of the major capsid protein VP1. This was observed in structure analyses of capsids encoded by many species and is often a consequence of environmental cues such as metal ions, changes to pH, or receptor/co-factor engagement. This review summarises the current understanding of P-domain flexibility, discussing the role this region plays in caliciviral infection and immune evasion, and highlighting potential avenues for further investigation.
History
DepositionNov 8, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52037.png

Downloads & links

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Map

FileDownload / File: emd_52037.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 600 pix.
= 623.4 Å		1.04 Å/pix.
x 600 pix.
= 623.4 Å		1.04 Å/pix.
x 600 pix.
= 623.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.039 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08284694 - 0.1582644
Average (Standard dev.)-0.0015207453 (±0.00832732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 623.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52037_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52037_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

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)
Virus shellShell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3

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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: 57.890055 KDa
Recombinant expressionOrganism: Macaca mulatta (Rhesus monkey)
SequenceString: MENSKTEQVT GATGITQSTV TAPLPEAVSS LSLAPTVNAL DPWVYLNQTE VPGGTFTVSS ATQPGSVLLE LEISPELNLY TSHLFRMYA GWSGGFSLKL LVAGNAFSAG KLIAAIIPPN IEVPNSAYLL TGFPHEILDF RTADSMEIIA PDIKNIDYHF R GDKLGKLV ...String:
MENSKTEQVT 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 AGSVTGNPNW RYALLDLPDN PTFDPTLPPV PRGFCDWGSG VKS GNKQHL VCFTGKKFAG GFQDVDAHMW DYGDNETVGL DNTYQRTIYI SDPSLEKDAQ YLVIPMGVSG AANDDTVQVA PNCY GSWDY APTVAPPLGE QFVWFRSQLP ASKTTTTSGV NSVPVNVNAL MSPDLIRSAY 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

Concentration3 mg/mL
BufferpH: 7.2 / Details: Phosphat buffered saline
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3475 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER / Details: Prior calicivirus models
Final reconstructionNumber classes used: 75 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 340802
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial model generated using Model Angelo Refined Using Coot, Phenix and Isolde (in ChimeraX)
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9hc5:
Structure of Tulane virus

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