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- EMDB-2436: Cryo-EM reconstruction of empty enterovirus 71 in complex with a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2436
TitleCryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19
Map dataReconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
Sample
  • Sample: Reconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
  • Virus: Human enterovirus 71
  • Protein or peptide: EV19/5/C1-6/F1/C11
KeywordsEV71 / human / enterovirus 71 / virus / antibody / Fab / E19 / complex / neutralizing / pathogen / genome / release
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse) / Human enterovirus 71
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsPlevka P / Perera R / Cardosa J / Suksatu A / Kuhn RJ / Rossmann MG
CitationJournal: PROC.NAT.ACAD.SCI.USA / Year: 2014
Title: Neutralizing antibodies can initiate genome release from human enterovirus 71
Authors: Plevka P / Lim P-Y / Perera R / Cardosa J / Suksatu A / Kuhn RJ / Rossmann MG
History
DepositionAug 8, 2013-
Header (metadata) releaseSep 4, 2013-
Map releaseFeb 5, 2014-
UpdateFeb 19, 2014-
Current statusFeb 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4c10
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4c10
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2436.png

Downloads & links

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Map

FileDownload / File: emd_2436.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.48 Å/pix.
x 200 pix.
= 496. Å		2.48 Å/pix.
x 200 pix.
= 496. Å		2.48 Å/pix.
x 200 pix.
= 496. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.7741611 - 4.40684891
Average (Standard dev.)0.02253945 (±0.90394598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.482.482.48
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z496.000496.000496.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-3.7744.4070.023

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Supplemental data

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Sample components

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Entire : Reconstruction of human enterovirus 71 with bound Fab fragments o...

EntireName: Reconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
Components
  • Sample: Reconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
  • Virus: Human enterovirus 71
  • Protein or peptide: EV19/5/C1-6/F1/C11

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Supramolecule #1000: Reconstruction of human enterovirus 71 with bound Fab fragments o...

SupramoleculeName: Reconstruction of human enterovirus 71 with bound Fab fragments of antibody E19
type: sample / ID: 1000
Oligomeric state: Icosahedral virus and 60 copies of bound Fab
Number unique components: 2
Molecular weightTheoretical: 6.8 MDa

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Supramolecule #1: Human enterovirus 71

SupramoleculeName: Human enterovirus 71 / type: virus / ID: 1 / Name.synonym: EV71 / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: EV71 / Sci species serotype: EV-174
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 3.2 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 280 Å / T number (triangulation number): 1

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Macromolecule #1: EV19/5/C1-6/F1/C11

MacromoleculeName: EV19/5/C1-6/F1/C11 / type: protein_or_peptide / ID: 1 / Name.synonym: E19 / Number of copies: 60 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / synonym: house mouse
Molecular weightTheoretical: 4.6 KDa

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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

Concentration2 mg/mL
BufferpH: 8 / Details: 10 mM Tris-HCl, pH 8.0, 0.5 M NaCl, and 1 mM EDTA
GridDetails: Quantifoin R1.2/1.3 Holey carbon 200Mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 2 second before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureMin: 95 K / Max: 120 K / Average: 119 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateSep 16, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 142 / Average electron dose: 18 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsParticles were boxed with e2boxer.py
CTF correctionDetails: CTF determined for all particles from one film, phase flip
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: eman, eman2 / Number images used: 10833
Final two d classificationNumber classes: 122

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Atomic model buiding 1

Initial modelPDB ID:

3zfe


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: EMFit
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Rcrit
Output model

PDB-4c10:
Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19

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Atomic model buiding 2

Initial modelPDB ID:

1qgc


Chain - Chain ID: 5
SoftwareName: EMFit
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Rcrit
Output model

PDB-4c10:
Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19

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