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- EMDB-0632: Rotavirus A-VP3 (RVA-VP3) -

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Basic information

Entry
Database: EMDB / ID: EMD-0632
TitleRotavirus A-VP3 (RVA-VP3)
Map dataA sub-atomic resolution cryo-EM structure of full-length Rotavirus A-VP3 (RVA-VP3)
Sample
  • Complex: VP3
    • Protein or peptide: Protein VP3
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE
KeywordsRotavirus / Capping enzyme / Methyl transferase / RTPase / PDE / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / viral process / mRNA guanylyltransferase activity / viral nucleocapsid / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / symbiont-mediated suppression of host innate immune response / GTP binding / RNA binding
Similarity search - Function
Protein VP3, rotavirus / Rotavirus VP3 protein / Viral protein 3 containing mRNA (guanine-N(7)-)-methyltransferase family profile.
Similarity search - Domain/homology
Biological speciesRotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKumar D / Yu X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
Welch FoundationQ-1967-20180324 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: To Be Published
Title: A sub-atomic resolution cryo-EM of full-length Rotavirus A-VP3 (RVA-VP3)
Authors: Kumar D / Yu X / Prasad V / Wang Z
History
DepositionMar 5, 2019-
Header (metadata) releaseApr 3, 2019-
Map releaseMar 11, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o6b
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0632.png

Downloads & links

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Map

FileDownload / File: emd_0632.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA sub-atomic resolution cryo-EM structure of full-length Rotavirus A-VP3 (RVA-VP3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 180 pix.
= 150.66 Å		0.84 Å/pix.
x 180 pix.
= 150.66 Å		0.84 Å/pix.
x 180 pix.
= 150.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.051173538 - 0.09492726
Average (Standard dev.)0.0009220303 (±0.008630419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 150.66 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z150.660150.660150.660
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0510.0950.001

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Supplemental data

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Half map: Half map of VP3

Fileemd_0632_half_map_1.map
AnnotationHalf map of VP3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of VP3

Fileemd_0632_half_map_2.map
AnnotationHalf map of VP3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VP3

EntireName: VP3
Components
  • Complex: VP3
    • Protein or peptide: Protein VP3
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE

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Supramolecule #1: VP3

SupramoleculeName: VP3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rotavirus A

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Macromolecule #1: Protein VP3

MacromoleculeName: Protein VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
Source (natural)Organism: Rotavirus A
Molecular weightTheoretical: 97.70382 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKVLALRHSV AQVYADTQIY THDDTKDSYE NAFLISNLTT HNILYFNYSA RTLEILNKSG IAAIEIQSLE ELFTLIRCNF TYDYENNVV YLHDYSYYTN NEIRTDQHWI TKTNIEEYLL PGWKLTYVGY NGNDTRGHYN FSFTCQNAAT DDDIIIEYIY S EALDFQNF ...String:
MKVLALRHSV AQVYADTQIY THDDTKDSYE NAFLISNLTT HNILYFNYSA RTLEILNKSG IAAIEIQSLE ELFTLIRCNF TYDYENNVV YLHDYSYYTN NEIRTDQHWI TKTNIEEYLL PGWKLTYVGY NGNDTRGHYN FSFTCQNAAT DDDIIIEYIY S EALDFQNF MLRKIKERMT TSLPIARLSN RVFRDKLFPL LVKKHKRVVN VGPRNESMFT FLNFPSIRQF SNGPYLVKNT IK LKQERWL GKRVSQFDIG QYKNMLNVIT TIYHYYNLYQ EKPIIYMVGS APSYWIYDVR QYSDFLFETW DPLDTPYSSI HHK ELFFAK DIGKLKDNSI LYIDIRTDRG NADWKEWRKV VELQTISNLN LAYQYLATGK SKVCCVKLTA MDLELPVSAK LLHH PTTEI RSEFYLLLDI WDVNNIKRFI PKGALYSFIN NVITDNVFIQ SPFKIRTSVS DYIVALYALS NDFNNREDII NLINN QKQS LITVRINNTF KDEPKVGFKS IYDWTFLPTD FETTNAIVTS YDGCLGIFGL SISLASKPTG NNHLFILNGT DKYYKL DQF ANHTGISRRS HQVRFSESAT SYSGYIFRDL SNSNFNLIGT NVENSVSGHV YNALIYYRYN YSFDLKRWIY LHSVEKA NI EGGKYYEHAP IELIYACKSA KEFASLQDDL TVLRYANEIE NYINKVYSIT YADDPNYFIG IKFNNIPYIY DVKVPHLT F GVLYISDNMI PDVVKIMKSM KQELFGMDVT TSYTYMLSDG VYVANVSGVL ATYFKMYNLF YKNQITFGQS RMFIPHITL SFSNNKTVRI ETTKLRIKSI YLRKIRGDTV FDMPE

UniProtKB: Protein VP3

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Macromolecule #2: GUANOSINE-5'-MONOPHOSPHATE

MacromoleculeName: GUANOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: 5GP
Molecular weightTheoretical: 363.221 Da
Chemical component information

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

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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

Concentration0.5 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000

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Image processing

Particle selectionNumber selected: 133712
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 70892
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 2.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0)

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