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- EMDB-3528: nora virus structure -

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Basic information

Entry
Database: EMDB / ID: EMD-3528
Titlenora virus structure
Map datanora virus b-factor corrected map.
Sample
  • Virus: Nora virus
    • Protein or peptide: capsid protein VP4C
    • Protein or peptide: capsid protein VP4B
    • Protein or peptide: Capsid protein VP4A
Function / homologyviral capsid / Capsid protein / ORF4 polyprotein
Function and homology information
Biological speciesNora virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLaurinmaki P / Shakeel S / Ekstrom J-O / Butcher SJ
Funding support Finland, 3 items
OrganizationGrant numberCountry
Academy of Finland139178 Finland
Academy of Finland275199 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Sci Rep / Year: 2020
Title: Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy.
Authors: Pasi Laurinmäki / Shabih Shakeel / Jens-Ola Ekström / Pezhman Mohammadi / Dan Hultmark / Sarah J Butcher /
Abstract: Nora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for ...Nora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for virus replication, but the capsid structure was at the time for genome publication unknown. By solving the structure of the virus, and through sequence comparison, we clear up this taxonomic ambiguity in the invertebrate RNA virosphere. Despite the lack of detectable similarity in the amino acid sequences, the 2.7 Å resolution cryoEM map showed Nora virus to have T = 1 symmetry with the characteristic capsid protein β-barrels found in all the viruses in the Picornavirales order. Strikingly, α-helical bundles formed from the extended C-termini of capsid protein VP4B and VP4C protrude from the capsid surface. They are similar to signalling molecule folds and implicated in virus entry. Unlike other viruses of Picornavirales, no intra-pentamer stabilizing annulus was seen, instead the intra-pentamer stability comes from the interaction of VP4C and VP4B N-termini. Finally, intertwining of the N-termini of two-fold symmetry-related VP4A capsid proteins and RNA, provides inter-pentamer stability. Based on its distinct structural elements and the genetic distance to other picorna-like viruses we propose that Nora virus, and a small group of related viruses, should have its own family within the order Picornavirales.
History
DepositionDec 8, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseDec 20, 2017-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3528.png

Downloads & links

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Map

FileDownload / File: emd_3528.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnora virus b-factor corrected map.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.04889733 - 0.11284691
Average (Standard dev.)0.0005152229 (±0.007036079)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0490.1130.001

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Supplemental data

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Mask #1

Fileemd_3528_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: nora virus, not b-factor corrected

Fileemd_3528_additional.map
Annotationnora virus, not b-factor corrected
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_3528_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_3528_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 : Nora virus

EntireName: Nora virus
Components
  • Virus: Nora virus
    • Protein or peptide: capsid protein VP4C
    • Protein or peptide: capsid protein VP4B
    • Protein or peptide: Capsid protein VP4A

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Supramolecule #1: Nora virus

SupramoleculeName: Nora virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Drosophila Nora virus strain Umea 2007 was derived from an infectious cDNA clone (accession GQ257737).
NCBI-ID: 363716 / Sci species name: Nora virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Drosophila melanogaster (fruit fly)
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: capsid protein VP4C

MacromoleculeName: capsid protein VP4C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nora virus
Molecular weightTheoretical: 45.258152 KDa
SequenceString: SLPENAPNAV SNPQQFITPA TALSAEEYNV HEALGETEEL ELDEFPVLVF KGNVPVDSVT SIPLDLATIY DFAWDGEQNA ISQKFQRFA HLIPKSAGGF GPVIGNYTIT ANLPTGVAGR ILHNCLPGDC VDLAVSRIFG LKSLLGVAGT AVSAIGGPLL N GLVNTAAP ...String:
SLPENAPNAV SNPQQFITPA TALSAEEYNV HEALGETEEL ELDEFPVLVF KGNVPVDSVT SIPLDLATIY DFAWDGEQNA ISQKFQRFA HLIPKSAGGF GPVIGNYTIT ANLPTGVAGR ILHNCLPGDC VDLAVSRIFG LKSLLGVAGT AVSAIGGPLL N GLVNTAAP ILSGAAHAIG GNVVGGLADA VIDIGSNLLT PKEKEQPSAN SSAISGDIPI SRFVEMLKYV KENYQDNPVF PT LLVEPQN FISNAMTALK TIPIEVFANM RNVKVERNLF DRTVVPTVKE ATLADIVIPN HMYGYILRDF LQNKRAFQSG TKQ NVYFQQ FLTVLSQRNI RTHITLNDIT SCSIDSESIA NKIERVKHYL STNSSGETTE EFSRTDTGLL PITTRKIVLG ESKR RTERY VAETVFPSVR Q

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Macromolecule #2: capsid protein VP4B

MacromoleculeName: capsid protein VP4B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nora virus
Molecular weightTheoretical: 28.166934 KDa
SequenceString: ADNEVTAEGG KLVQELVYDH SAIPVAPVVE TQAEQPEVPV SLVATRKNDT GHLATKWYDF AKISLSNPAN MNWTTLTIDP YNNVTLSRD GESMVLPWRR NVWTTGSKSI GYIRTMVAQI NIPRPPQISG VLEVKDSINN SSISLVEFGG KVEIPIIPKV M NGLATTAS ...String:
ADNEVTAEGG KLVQELVYDH SAIPVAPVVE TQAEQPEVPV SLVATRKNDT GHLATKWYDF AKISLSNPAN MNWTTLTIDP YNNVTLSRD GESMVLPWRR NVWTTGSKSI GYIRTMVAQI NIPRPPQISG VLEVKDSINN SSISLVEFGG KVEIPIIPKV M NGLATTAS LPRHRLNPWM RTAESKVELQ YRIIAFNRTS DIADLNVSVL LRPGDSQFQL PMKPDNNVDT RHFELVEALM YH YDSLRIR GEEQ

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Macromolecule #3: Capsid protein VP4A

MacromoleculeName: Capsid protein VP4A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nora virus
Molecular weightTheoretical: 29.019826 KDa
SequenceString: MQNPTQTMHI YDMPLRVIAG LSTLAKTTEE DDNTSTGIVV SEVGEPQVVN HPAWIDPFVA YQLRAPRKNI TPDFIFGRAD IGNAFSAFL PRRFSAPAVG TRLVVDPVFT YQQRTVLGLY NYFHADFYYI VHVPAPLGTG IYLKIYAPEF DTTTVTRGIR F KPSASPTI ...String:
MQNPTQTMHI YDMPLRVIAG LSTLAKTTEE DDNTSTGIVV SEVGEPQVVN HPAWIDPFVA YQLRAPRKNI TPDFIFGRAD IGNAFSAFL PRRFSAPAVG TRLVVDPVFT YQQRTVLGLY NYFHADFYYI VHVPAPLGTG IYLKIYAPEF DTTTVTRGIR F KPSASPTI ALSVPWSNDL STVETSVGRV GQSGGSIVIE TIEDNSNETV NTPLSITVWC CMANIKATGY RHADTSAYNE KG MNFIPVP VPKPPVPPTK PITGEEQ

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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 / Details: 10mM Tris-HCl pH 7.4.
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Specialist opticsEnergy filter - Name: GIF Quantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3516 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 30313
Startup modelType of model: OTHER
Details: Initial map was generated using random model generation (RMC) in AUTO3DEM.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 16131
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-5mm2:
nora virus structure

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