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- EMDB-9634: The structure of Enterovirus D68 mature virion in complex with Fa... -

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Basic information

Entry
Database: EMDB / ID: 9634
TitleThe structure of Enterovirus D68 mature virion in complex with Fab 15C5 and 11G1
Map data
SampleEnterovirus D68Enterovirus 68:
virus / VL of Fab 11G1 / VH of Fab 11G1 / VL of Fab 15C5 / VH of Fab 15C5 / (Capsid protein ...Capsid) x 3
Function / homologyHelicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like ...Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / AAA+ ATPase domain / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA-directed RNA polymerase, catalytic domain / 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 / RNA dependent RNA polymerase / Peptidase C3, picornavirus core protein 2A / 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-triphosphatase / viral capsid / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / suppression by virus of host gene expression / protein complex oligomerization / peptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / viral process / structural molecule activity / RNA binding / transcription, DNA-templated / membrane / ATP binding / Genome polyprotein / Polyprotein
Function and homology information
SourceEnterovirus D68 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsZheng QB / Zhu R / Xu LF / He MZ / Yan XD / Cheng T / Li SW
CitationJournal: Nat Microbiol / Year: 2018
Title: Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization
Authors: Zheng QB / Zhu R / Xu LF / He MZ / Yan XD / Cheng T / Li SW
Validation ReportPDB-ID: 6aj9

SummaryFull reportAbout validation report
DateDeposition: Aug 27, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.0339
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.0339
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6aj9
  • Surface level: 0.0339
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6aj9
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9634.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:0.0339 (by author), 0.0339 (movie #1):
Minimum - Maximum-0.15490171 - 0.26183948
Average (Standard dev.)0.000121504716 (0.010316445)
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/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.1550.2620.000

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Supplemental data

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Sample components

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Entire Enterovirus D68

EntireName: Enterovirus D68 / Number of components: 8

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Component #1: virus, Enterovirus D68

VirusName: Enterovirus D68Enterovirus 68 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Enterovirus D68

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Component #2: protein, VL of Fab 11G1

ProteinName: VL of Fab 11G1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.625044 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #3: protein, VH of Fab 11G1

ProteinName: VH of Fab 11G1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.517063 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #4: protein, VL of Fab 15C5

ProteinName: VL of Fab 15C5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.656906 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #5: protein, VH of Fab 15C5

ProteinName: VH of Fab 15C5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.027412 kDa
SourceSpecies: Mus musculus (house mouse)

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Component #6: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.673035 kDa
SourceSpecies: Enterovirus D68

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Component #7: protein, Capsid protein VP2

ProteinName: Capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.567135 kDa
SourceSpecies: Enterovirus D68

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Component #8: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.142842 kDa
SourceSpecies: Enterovirus D68

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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 / Number of projections: 102512
3D reconstructionSoftware: RELION / Resolution: 3.5 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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