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- PDB-6mjz: Cryo-EM structure of Human Parainfluenza Virus Type 3 (hPIV3) in ... -

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Basic information

Entry
Database: PDB / ID: 6mjz
TitleCryo-EM structure of Human Parainfluenza Virus Type 3 (hPIV3) in complex with antibody PIA174
Components
  • Fusion glycoprotein F0
  • PIA174 Fab Heavy chain
  • PIA174 Fab Light chain
KeywordsVIRAL PROTEIN/immune system / hPIV3 Envelope / asymmetric / complex / antibody / VIRAL PROTEIN / VIRAL PROTEIN-immune system complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman parainfluenza virus 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAcharya, P. / Stewart-Jones, G. / Carragher, B. / Potter, C.S. / Kwong, P.D.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure-based design of a quadrivalent fusion glycoprotein vaccine for human parainfluenza virus types 1-4.
Authors: Guillaume B E Stewart-Jones / Gwo-Yu Chuang / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Yaroslav Tsybovsky / Li Ou / Baoshan Zhang / Blanca Fernandez-Rodriguez / Valentina Gilardi / ...Authors: Guillaume B E Stewart-Jones / Gwo-Yu Chuang / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Yaroslav Tsybovsky / Li Ou / Baoshan Zhang / Blanca Fernandez-Rodriguez / Valentina Gilardi / Chiara Silacci-Fregni / Martina Beltramello / Ulrich Baxa / Aliaksandr Druz / Wing-Pui Kong / Paul V Thomas / Yongping Yang / Kathryn E Foulds / John-Paul Todd / Hui Wei / Andres M Salazar / Diana G Scorpio / Bridget Carragher / Clinton S Potter / Davide Corti / John R Mascola / Antonio Lanzavecchia / Peter D Kwong /
Abstract: Parainfluenza virus types 1-4 (PIV1-4) are highly infectious human pathogens, of which PIV3 is most commonly responsible for severe respiratory illness in newborns, elderly, and immunocompromised ...Parainfluenza virus types 1-4 (PIV1-4) are highly infectious human pathogens, of which PIV3 is most commonly responsible for severe respiratory illness in newborns, elderly, and immunocompromised individuals. To obtain a vaccine effective against all four PIV types, we engineered mutations in each of the four PIV fusion (F) glycoproteins to stabilize their metastable prefusion states, as such stabilization had previously enabled the elicitation of high-titer neutralizing antibodies against the related respiratory syncytial virus. A cryoelectron microscopy structure of an engineered PIV3 F prefusion-stabilized trimer, bound to the prefusion-specific antibody PIA174, revealed atomic-level details for how introduced mutations improved stability as well as how a single PIA174 antibody recognized the trimeric apex of prefusion PIV3 F. Nine combinations of six newly identified disulfides and two cavity-filling mutations stabilized the prefusion PIV3 F immunogens and induced 200- to 500-fold higher neutralizing titers in mice than were elicited by PIV3 F in the postfusion conformation. For PIV1, PIV2, and PIV4, we also obtained stabilized prefusion Fs, for which prefusion versus postfusion titers were 2- to 20-fold higher. Elicited murine responses were PIV type-specific, with little cross-neutralization of other PIVs. In nonhuman primates (NHPs), quadrivalent immunization with prefusion-stabilized Fs from PIV1-4 consistently induced potent neutralizing responses against all four PIVs. For PIV3, the average elicited NHP titer from the quadrivalent immunization was more than fivefold higher than any titer observed in a cohort of over 100 human adults, highlighting the ability of a prefusion-stabilized immunogen to elicit especially potent neutralization.
History
DepositionSep 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
H: PIA174 Fab Heavy chain
L: PIA174 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)211,1115
Polymers211,1115
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fusion glycoprotein F0


Mass: 54970.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parainfluenza virus 3 / Gene: F, KMQ_34898gpF / Production host: Homo sapiens (human) / References: UniProt: A0A059QA82
#2: Antibody PIA174 Fab Heavy chain


Mass: 23512.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody PIA174 Fab Light chain


Mass: 22686.240 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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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

ComponentName: Complex of hPIV3 Env Q162C-L168C, I213C-G230C, A463V, I474Y in complex with antibody PIA174
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Human respirovirus 3
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.4 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97177 / Symmetry type: POINT
RefinementHighest resolution: 4.3 Å

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