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- EMDB-27765: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmet... -

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Basic information

Entry
Database: EMDB / ID: EMD-27765
TitleChikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
Map dataChikungunya VLP in complex with neutralizing Fab 506.C01
Sample
  • Complex: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: 506.C01 light chain
    • Protein or peptide: 506.C01 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / VIRAL PROTEIN-IMMUNE SYSTEM complex / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain Senegal 37997 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsAdams LJ / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00062 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Sci Transl Med / Year: 2023
Title: A chikungunya virus-like particle vaccine induces broadly neutralizing and protective antibodies against alphaviruses in humans.
Authors: Saravanan Raju / Lucas J Adams / James T Earnest / Kelly Warfield / Lo Vang / James E Crowe / Daved H Fremont / Michael S Diamond /
Abstract: Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes epidemics of acute and chronic musculoskeletal disease. Here, we analyzed the human B cell response to a CHIKV-like particle- ...Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes epidemics of acute and chronic musculoskeletal disease. Here, we analyzed the human B cell response to a CHIKV-like particle-adjuvanted vaccine (PXVX0317) from samples obtained from a phase 2 clinical trial in humans (NCT03483961). Immunization with PXVX0317 induced high levels of neutralizing antibody in serum against CHIKV and circulating antigen-specific B cells up to 6 months after immunization. Monoclonal antibodies (mAbs) generated from peripheral blood B cells of three PXVX0317-vaccinated individuals on day 57 after immunization potently neutralized CHIKV infection, and a subset of these inhibited multiple related arthritogenic alphaviruses. Epitope mapping and cryo-electron microscopy defined two broadly neutralizing mAbs that uniquely bind to the apex of the B domain of the E2 glycoprotein. These results demonstrate the inhibitory breadth and activity of the human B cell response induced by the PXVX0317 vaccine against CHIKV and potentially other related alphaviruses.
History
DepositionAug 2, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27765.png

Downloads & links

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Map

FileDownload / File: emd_27765.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya VLP in complex with neutralizing Fab 506.C01
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.017194908 - 2.4855917
Average (Standard dev.)0.005570057 (±0.047168568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 406.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_27765_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_27765_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_27765_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmet...

EntireName: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
Components
  • Complex: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: 506.C01 light chain
    • Protein or peptide: 506.C01 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmet...

SupramoleculeName: Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Chikungunya virus strain Senegal 37997

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 47.346715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNIP ISIDIPDAAF TRVVDAPSVT DMSCEVPACT HSSDFGGVAI IKY TASKKG KCAVHSMTNA VTIREADVEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAACHPPKDH IVNYPASHTT LGVQ DISTT AMSWVQKITG GVGLIVAVAA LILIVVLCVS FSRH

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Macromolecule #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 46.858312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP ...String:
NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP PDTPDRTLMT QQSGNVKITV NGQTVRYKCN CGGSNEGLTT TDKVINNCKI DQCHAAVTNH KNWQYNSPLV PR NAELGDR KGKIHIPFPL ANVTCRVPKA RNPTVTYGKN QVTMLLYPDH PTLLSYRNMG QEPNYHEEWV THKKEVTLTV PTE GLEVTW GNNEPYKYWP QMSTNGTAHG HPHEIILYYY ELYPTMTVVI VSVASFVLLS MVGTAVGMCV CARRRCITPY ELTP GATVP FLLSLLCCVR TTKA

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 16.458701 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NDCIFEVKHE GKVMGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

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Macromolecule #4: 506.C01 light chain

MacromoleculeName: 506.C01 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.486756 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS VSASVGDRVT ITCRASQGIS SWLGWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QANSFPRTFG QGTKVEIK

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Macromolecule #5: 506.C01 heavy chain

MacromoleculeName: 506.C01 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.0827 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSQTLSL TCTVSGGSIS SDDYYWTWIR LPPGKGLEWI GYIFYTGGTY YNPSLKSRVT ISLDRSKNQF SLKLSSVTA ADTAVYFCAR APETYCSTTN CYKGYFDSWG QGTLVTVSS

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 59000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 38.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 866369
FSC plot (resolution estimation)

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