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- PDB-6z3q: Structure of EV71 in complex with a protective antibody 38-1-10A Fab -

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Basic information

Entry
Database: PDB / ID: 6z3q
TitleStructure of EV71 in complex with a protective antibody 38-1-10A Fab
Components
  • Heavy chain
  • Light chain
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / EV71 / antibody 38-3-11A / antibody 38-1-10A / EV71-Fab complex
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 / viral capsid / nucleoside-triphosphate phosphatase / channel activity ...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 / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / 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 VP4 superfamily / 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 superfamily / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterovirus A71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhou, D. / Fry, E.E. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Structural and functional analysis of protective antibodies targeting the threefold plateau of enterovirus 71.
Authors: Kuan-Ying A Huang / Daming Zhou / Elizabeth E Fry / Abhay Kotecha / Peng-Nien Huang / Shu-Li Yang / Kuo-Chien Tsao / Yhu-Chering Huang / Tzou-Yien Lin / Jingshan Ren / David I Stuart /
Abstract: Enterovirus 71 (EV71)-neutralizing antibodies correlate with protection and have potential as therapeutic agents. We isolate and characterize a panel of plasmablast-derived monoclonal antibodies from ...Enterovirus 71 (EV71)-neutralizing antibodies correlate with protection and have potential as therapeutic agents. We isolate and characterize a panel of plasmablast-derived monoclonal antibodies from an infected child whose antibody response focuses on the plateau epitope near the icosahedral 3-fold axes. Eight of a total of 19 antibodies target this epitope and three of these potently neutralize the virus. Representative neutralizing antibodies 38-1-10A and 38-3-11A both confer effective protection against lethal EV71 challenge in hSCARB2-transgenic mice. The cryo-electron microscopy structures of the EV71 virion in complex with Fab fragments of these potent and protective antibodies reveal the details of a conserved epitope formed by residues in the BC and HI loops of VP2 and the BC and HI loops of VP3 spanning the region around the 3-fold axis. Remarkably, the two antibodies interact with the epitope in quite distinct ways. These plateau-binding antibodies provide templates for promising candidate therapeutics.
History
DepositionMay 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Sep 2, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7747
Polymers142,4746
Non-polymers2991
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
H: Heavy chain
L: Light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,566,418420
Polymers8,548,448360
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
D: VP4
H: Heavy chain
L: Light chain
hetero molecules
x 5


  • icosahedral pentamer
  • 714 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)713,86835
Polymers712,37130
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
H: Heavy chain
L: Light chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 857 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)856,64242
Polymers854,84536
Non-polymers1,7976
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1 / VP1


Mass: 32781.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71
References: UniProt: A0A2L1GIK5, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein VP2 / VP2


Mass: 27784.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / References: UniProt: D4QGA2
#3: Protein VP3 / VP3


Mass: 26540.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / References: UniProt: D4QGA3
#4: Protein VP4 / VP4


Mass: 6380.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / References: UniProt: Q6YLE3

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Antibody , 2 types, 2 molecules HL

#5: Antibody Heavy chain


Mass: 25216.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody Light chain


Mass: 23770.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Enterovirus A71 with Human antibodyVIRUS#1-#60MULTIPLE SOURCES
2Enterovirus A71COMPLEX#1-#41NATURAL
3Human antibodyCOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Enterovirus A7139054
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10074 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048464
ELECTRON MICROSCOPYf_angle_d0.5411550
ELECTRON MICROSCOPYf_dihedral_angle_d17.0193036
ELECTRON MICROSCOPYf_chiral_restr0.0441290
ELECTRON MICROSCOPYf_plane_restr0.0041490

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