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- EMDB-9604: The structure of CVA10 mature virion in complex with Fab 2G8 -

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Basic information

Entry
Database: EMDB / ID: 9604
TitleThe structure of CVA10 mature virion in complex with Fab 2G8
Map data
SampleCVA10 mature virion in complex with Fab 2G8:
virus / VL of Fab 2G8 / VH of Fab 2G8 / VP1 / VP2 / VP3 / VP4 / ligand
Function / homologyPeptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid ...Peptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / picornavirus capsid protein / RNA dependent RNA polymerase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / RNA helicase / P-loop containing nucleoside triphosphate hydrolase / 3C cysteine protease (picornain 3C) / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / suppression by virus of host gene expression / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Polyprotein
Function and homology information
SourceCoxsackievirus A10 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsZhu R / Zheng QB / Xu LF / Cui YX / Li SW / Yan XD / Zhou ZH / Cheng T
CitationJournal: Sci Adv / Year: 2018
Title: Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10.
Authors: Rui Zhu / Longfa Xu / Qingbing Zheng / Yanxiang Cui / Shaowei Li / Maozhou He / Zhichao Yin / Dongxiao Liu / Shuxuan Li / Zizhen Li / Zhenqin Chen / Hai Yu / Yuqiong Que / Che Liu / Zhibo Kong / Jun Zhang / Timothy S Baker / Xiaodong Yan / Z Hong Zhou / Tong Cheng / Ningshao Xia
Validation ReportPDB-ID: 6ad0

SummaryFull reportAbout validation report
DateDeposition: Jul 28, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0362
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0362
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ad0
  • Surface level: 0.0362
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ad0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9604.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.13 Å/pix.
= 676.8 Å
600 pix
1.13 Å/pix.
= 676.8 Å
600 pix
1.13 Å/pix.
= 676.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density
Contour Level:0.0362 (by author), 0.0362 (movie #1):
Minimum - Maximum-0.10955997 - 0.20438156
Average (Standard dev.)0.0005581341 (0.009421075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.00.00.0
Limit599.0599.0599.0
Spacing600600600
CellA=B=C: 676.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z676.800676.800676.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.1100.2040.001

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Supplemental data

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Sample components

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Entire CVA10 mature virion in complex with Fab 2G8

EntireName: CVA10 mature virion in complex with Fab 2G8 / Number of components: 8

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Component #1: virus, Coxsackievirus A10

VirusName: Coxsackievirus A10 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Coxsackievirus A10

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Component #2: protein, VL of Fab 2G8

ProteinName: VL of Fab 2G8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.391881 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #3: protein, VH of Fab 2G8

ProteinName: VH of Fab 2G8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.149508 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #4: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.15923 kDa
SourceSpecies: Coxsackievirus A10

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Component #5: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.808133 kDa
SourceSpecies: Coxsackievirus A10

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Component #6: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.129588 kDa
SourceSpecies: Coxsackievirus A10

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Component #7: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.464104 kDa
SourceSpecies: Coxsackievirus A10

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Component #8: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 36555
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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