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- EMDB-62263: Structural Basis for the Recognition of Blood Group Trisaccharide... -

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Basic information

Entry
Database: EMDB / ID: EMD-62263
TitleStructural Basis for the Recognition of Blood Group Trisaccharides by Tulane virus
Map data
Sample
  • Complex: VP1
    • Protein or peptide: Capsid protein
KeywordsVP1 / VIRAL PROTEIN
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Capsid protein
Function and homology information
Biological speciesRhesus macaque recovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsQian Y / Cong Y / Li X / Chen Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Basis for the Recognition of Blood Group Trisaccharides by Tulane virus
Authors: Qian Y / Cong J / Li X / Chen Y
History
DepositionNov 3, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62263.png

Downloads & links

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Map

FileDownload / File: emd_62263.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 220 pix.
= 299.2 Å		1.36 Å/pix.
x 220 pix.
= 299.2 Å		1.36 Å/pix.
x 220 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.05703644 - 0.11556179
Average (Standard dev.)0.00084545976 (±0.00759878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62263_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_62263_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VP1

EntireName: VP1
Components
  • Complex: VP1
    • Protein or peptide: Capsid protein

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Supramolecule #1: VP1

SupramoleculeName: VP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhesus macaque recovirus

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhesus macaque recovirus
Molecular weightTheoretical: 57.744688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MESTTEVTGA TGVVTNVAAA PLPEATSSMS LAPTVNSIDP WIFLNPTEVP GGTFTVASNT QPGTMLLDIE ISPELNIFTA HMFRMYAGW SGGFAIKLLV AGNAFSAGKL IVAIIPPNVQ VPNSAYLLTG FPHEILDFRT ADQVEIIAPD IKNLDYHFRG D KLGRLVVM ...String:
MESTTEVTGA TGVVTNVAAA PLPEATSSMS LAPTVNSIDP WIFLNPTEVP GGTFTVASNT QPGTMLLDIE ISPELNIFTA HMFRMYAGW SGGFAIKLLV AGNAFSAGKL IVAIIPPNVQ VPNSAYLLTG FPHEILDFRT ADQVEIIAPD IKNLDYHFRG D KLGRLVVM VYSPLRSTAT DFEIEIKLLS APLPDFKFTM LVPPVQNNAL PIWQIPPTPP GAMVNPRSPL TPVVDLYINS SW TTCNHQL GRYTIDGGAI GNSTFNPSGL WTGTFTAESG SVSGQTNWRI AMLDNPYNPT SDPTLPPVPR GFCDWGSGVK SGA RQHLVC FTGVETDNGE GYKDVDAHMW DYGDDATIGL DNTYQRQIYI SDPTALDSGK RYIIIPMGAS GSATDDTLQI SPNC YGSWD YAPTIAPPLG EQIVWFRSYL PASSTSASSG VNSVSAHISS LMSPDLIRSA YVSGFPEGKA ALLDYVLYGG SVVEQ FKMY REGYLTANAT GTNTGFIIPP DGYFRFNSWV SPTFVIGNVV DLSSSRSLTF H

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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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