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- EMDB-28058: Venezuelan equine encephalitis virus-like particle in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-28058
TitleVenezuelan equine encephalitis virus-like particle in complex with Fab SKT05, local refinement
Map dataMap obtained using DeepEMHancer
Sample
  • Complex: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05
    • Protein or peptide: Coat protein
    • Protein or peptide: Fab SKT05 heavy chain
    • Protein or peptide: Fab SKT05 light chain
KeywordsVenezuelan equine encephalitis virus / neutralizing antibody / VEEV / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 speciesVenezuelan equine encephalitis virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsTsybovsky Y / Pletnev S / Verardi R / Roederer M / Kwong PD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Vaccine elicitation and structural basis for antibody protection against alphaviruses.
Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / ...Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / Raffaello Verardi / Baoshan Zhang / David Ambrozak / Margaret Beddall / Hong Lei / Eun Sung Yang / Tracy Liu / Amy R Henry / Reda Rawi / Arne Schön / Chaim A Schramm / Chen-Hsiang Shen / Wei Shi / Tyler Stephens / Yongping Yang / Maria Burgos Florez / Julie E Ledgerwood / Crystal W Burke / Lawrence Shapiro / Julie M Fox / Peter D Kwong / Mario Roederer /
Abstract: Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine ...Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses.
History
DepositionSep 7, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28058.png

Downloads & links

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Map

FileDownload / File: emd_28058.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap obtained using DeepEMHancer
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.064076364 - 1.8054425
Average (Standard dev.)0.0022564689 (±0.030926416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 312.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map before post-processing

Fileemd_28058_additional_1.map
AnnotationMap before post-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map obtained using standard post-processing in Relion

Fileemd_28058_additional_2.map
AnnotationMap obtained using standard post-processing in Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_28058_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_28058_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between Venezuelan equine encephalitis virus-like particl...

EntireName: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05
Components
  • Complex: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05
    • Protein or peptide: Coat protein
    • Protein or peptide: Fab SKT05 heavy chain
    • Protein or peptide: Fab SKT05 light chain

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Supramolecule #1: Complex between Venezuelan equine encephalitis virus-like particl...

SupramoleculeName: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The map was obtained using symmetry expansion and signal subtraction. DeepEMHancer was used for post-processing.
Source (natural)Organism: Venezuelan equine encephalitis virus
Molecular weightTheoretical: 33 MDa

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
Molecular weightTheoretical: 138.662531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK ...String:
MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK KASKYDLEYA DVPQNMRADT FKYTHEKPQG YYSWHHGAVQ YENGRFTVPK GVGAKGDSGR PILDNQGRVV AI VLGGVNE GSRTALSVVM WNEKGVTVKY TPENCEQWSL VTTMCLLANV TFPCAQPPIC YDRKPAETLA MLSVNVDNPG YDE LLEAAV KCPGRKRRST EELFNEYKLT RPYMARCIRC AVGSCHSPIA IEAVKSDGHD GYVRLQTSSQ YGLDSSGNLK GRTM RYDMH GTIKEIPLHQ VSLYTSRPCH IVDGHGYFLL ARCPAGDSIT MEFKKDSVRH SCSVPYEVKF NPVGRELYTH PPEHG VEQA CQVYAHDAQN RGAYVEMHLP GSEVDSSLVS LSGSSVTVTP PDGTSALVEC ECGGTKISET INKTKQFSQC TKKEQC RAY RLQNDKWVYN SDKLPKAAGA TLKGKLHVPF LLADGKCTVP LAPEPMITFG FRSVSLKLHP KNPTYLITRQ LADEPHY TH ELISEPAVRN FTVTEKGWEF VWGNHPPKRF WAQETAPGNP HGLPHEVITH YYHRYPMSTI LGLSICAAIA TVSVAAST W LFCRSRVACL TPYRLTPNAR IPFCLAVLCC ARTARAETTW ESLDHLWNNN QQMFWIQLLI PLAALIVVTR LLRCVCCVV PFLVMAGAAA PAYEHATTMP SQAGISYNTI VNRAGYAPLP ISITPTKIKL IPTVNLEYVT CHYKTGMDSP AIKCCGSQEC TPTYRPDEQ CKVFTGVYPF MWGGAYCFCD TENTQVSKAY VMKSDDCLAD HAEAYKAHTA SVQAFLNITV GEHSIVTTVY V NGETPVNF NGVKITAGPL STAWTPFDRK IVQYAGEIYN YDFPEYGAGQ PGAFGDIQSR TVSSSDLYAN TNLVLQRPKA GA IHVPYTQ APSGFEQWKK DKAPSLKFTA PFGCEIYTNP IRAENCAVGS IPLAFDIPDA LFTRVSETPT LSAAECTLNE CVY SSDFGG IATVKYSASK SGKCAVHVPS GTATLKEAAV ELTEQGSATI HFSTANIHPE FRLQICTSYV TCKGDCHPPK DHIV THPQY HAQTFTAAVS KTAWTWLTSL LGGSAVIIII GLVLATIVAM YVLTNQKHN

UniProtKB: Structural polyprotein

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Macromolecule #2: Fab SKT05 heavy chain

MacromoleculeName: Fab SKT05 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 25.517631 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLK TEDTAVYYCT RDDRTSCRRG VCYAAFHSWG QGVLVTVSSA STKGPSVFPL APSSRSTSES TAALGCLVKD Y FPEPVTVS ...String:
EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLK TEDTAVYYCT RDDRTSCRRG VCYAAFHSWG QGVLVTVSSA STKGPSVFPL APSSRSTSES TAALGCLVKD Y FPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVEI KTCGGLEVLF Q

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Macromolecule #3: Fab SKT05 light chain

MacromoleculeName: Fab SKT05 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.238729 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCL QYDSPPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCL QYDSPPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4068840
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: The map was obtained using symmetry expansion and signal subtraction. DeepEMHancer was used for post-processing.
Number images used: 190096
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-8eeu:
Venezuelan equine encephalitis virus-like particle in complex with Fab SKT05

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