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- EMDB-28056: Venezuelan equine encephalitis virus-like particle in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-28056
TitleVenezuelan equine encephalitis virus-like particle in complex with Fab SKT05
Map dataFinal map after post-processing
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
Biological speciesVenezuelan equine encephalitis virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_28056.png

Downloads & links

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Map

FileDownload / File: emd_28056.map.gz / Format: CCP4 / Size: 2.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map after post-processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 920 pix.
= 971.52 Å		1.06 Å/pix.
x 920 pix.
= 971.52 Å		1.06 Å/pix.
x 920 pix.
= 971.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.007927649 - 0.022417046
Average (Standard dev.)0.00033501803 (±0.0012218959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions920920920
Spacing920920920
CellA=B=C: 971.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28056_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_28056_additional_1.map
AnnotationMap before post-processing
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_28056_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_28056_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
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 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKE ASQKQKGGGQ GKKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTF PIMLEGKING YACVVGGKLF RPMHVEGKID NDVLAALKTK ...String:
MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKE ASQKQKGGGQ GKKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTF PIMLEGKING YACVVGGKLF RPMHVEGKID NDVLAALKTK KASKYDLEYA DV PQNMRAD TFKYTHEKPQ GYYSWHHGAV QYENGRFTVP KGVGAKGDSG RPILDNQGRV VAI VLGGVN EGSRTALSVV MWNEKGVTVK YTPENCEQW SLVTTMCLLA NVTFPCAQPP ICYDR KPAE TLAMLSVNVD NPGYDELLEA AVKCPGRKRR STEELFNEY KLTRPYMARC IRCAVGS CH SPIAIEAVKS DGHDGYVRLQ TSSQYGLDSS GNLKGRTMRY DMHGTIKEIP LHQVSLYT S RPCHIVDGHG YFLLARCPAG DSITMEFKKD SVRHSCSVPY EVKFNPVGRE LYTHPPEHG VEQACQVYAH DAQNRGAYVE MHLPGSEVDS SLVSLSGSSV TVTPPDGTSA LVECECGGTK ISETINKTK QFSQCTKKEQ CRAYRLQNDK WVYNSDKLPK AAGATLKGKL HVPFLLADGK C TVPLAPEP MITFGFRSVS LKLHPKNPTY LITRQLADEP HYTHELISEP AVRNFTVTEK GW EFVWGNH PPKRFWAQET APGNPHGLPH EVITHYYHRY PMSTILGLSI CAAIATVSVA AST WLFCRS RVACLTPYRL TPNARIPFCL AVLCCARTAR AETTWESLDH LWNNNQQMFW IQLL IPLAA LIVVTRLLRC VCCVVPFLVM AGAAAPA YE HATTMPSQAG ISYNTIVNRA GYAPLP ISI TPTKIKLIPT VNLEYVTCHY KTGMDSPAIK CCGSQECTPT YRPDEQCKVF TGVYPFM WG GAYCFCDTEN TQVSKAYVMK SDDCLADHAE AYKAHTASVQ AFLNITVGEH SIVTTVYV N GETPVNFNGV KITAGPLSTA WTPFDRKIVQ YAGEIYNYDF PEYGAGQPGA FGDIQSRTV SSSDLYANTN LVLQRPKAGA IHVPYTQAPS GFEQWKKDKA PSLKFTAPFG CEIYTNPIRA ENCAVGSIP LAFDIPDALF TRVSETPTLS AAECTLNECV YSSDFGGIAT VKYSASKSGK C AVHVPSGT ATLKEAAVEL TEQGSATIHF STANIHPEFR LQICTSYVTC KGDCHPPKDH IV THPQYHA QTFTAAVSKT AWTWLTSLLG GSAVIIIIGL VLATIVAMYV LTNQKHN

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Macromolecule #2: Fab SKT05 heavy chain

MacromoleculeName: Fab SKT05 heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLKT EDTAVYYCTR DDRTSCRRGV CYAAFHSWGQ GVLVTVSS A STKGPSVFPL APSSRSTSES TAALGCLVKD YFPEPVTVSW ...String:
EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLKT EDTAVYYCTR DDRTSCRRGV CYAAFHSWGQ GVLVTVSS A STKGPSVFPL APSSRSTSES TAALGCLVKD YFPEPVTVSW NSGSLTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY VCNVNHKPSN TKVDKRVEIK TCGglevlfq

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Macromolecule #3: Fab SKT05 light chain

MacromoleculeName: Fab SKT05 light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCLQ YDSPPFTFGP GTKVEIK RT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS QESVTEQDSK ...String:
DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCLQ YDSPPFTFGP GTKVEIK RT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS QESVTEQDSK DNTYSLSSTL TLSSTEYQSH KVYACEVTHQ GLSSPVTKSF NRGEC

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 172425
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 67814
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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