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- EMDB-27722: Cryo-EM Structure of Antibody SKT05 in complex with Western Equin... -

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Basic information

Entry
Database: EMDB / ID: EMD-27722
TitleCryo-EM Structure of Antibody SKT05 in complex with Western Equine Encephalitis Virus spike (local refinement from VLP particles)
Map data
Sample
  • Complex: Western Equine Encephalitis Virus trimer in complex with Antibody Fab SKT05
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Antibody Fab SKT05 heavy chain
    • Protein or peptide: Antibody Fab SKT05 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / SKT05 / Western Equine Encephalitis Virus / broadly neutralizing / IMMUNE SYSTEM
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / 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 / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / 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 / virion attachment to host cell / host cell plasma membrane / structural molecule activity / 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 speciesWestern equine encephalitis virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
AuthorsCerutti G / Verardi R / Roederer M / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
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
DepositionJul 27, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27722.png

Downloads & links

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Map

FileDownload / File: emd_27722.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 640 pix.
= 1062.4 Å		1.66 Å/pix.
x 640 pix.
= 1062.4 Å		1.66 Å/pix.
x 640 pix.
= 1062.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.7105643 - 4.0652547
Average (Standard dev.)-0.00011137868 (±0.032254092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1062.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27722_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27722_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Western Equine Encephalitis Virus trimer in complex with Antibody...

EntireName: Western Equine Encephalitis Virus trimer in complex with Antibody Fab SKT05
Components
  • Complex: Western Equine Encephalitis Virus trimer in complex with Antibody Fab SKT05
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Antibody Fab SKT05 heavy chain
    • Protein or peptide: Antibody Fab SKT05 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Western Equine Encephalitis Virus trimer in complex with Antibody...

SupramoleculeName: Western Equine Encephalitis Virus trimer in complex with Antibody Fab SKT05
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Western equine encephalitis virus

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Macromolecule #1: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 45.29373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM DKIAISTSGP CRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK ETSAGYITMH R PGPHAYKS ...String:
PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM DKIAISTSGP CRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK ETSAGYITMH R PGPHAYKS YLEEASGEVY IKPPSGKNVT YECKCGDYST GIVSTRTKMN GCTKAKQCIA YKSDQTKWVF NSPDLIRHTD HS VQGKLHI PFRLTPTVCP VPLAHTPTVT KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFSVGREGLE YVW GNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPYALAPNA TVPT ALAVL CCI

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Macromolecule #2: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 52.905348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RPTNAETFGE TLNHLWFNNQ PFLWAQLCIP LAALVILFRC FSCCMPFLLV AGVCLGKVDA FEHATTVPNV PGIPYKALVE RAGYAPLNL EITVVSSELT PSTNKEYVTC RFHTVIPSPQ VKCCGSLECK ASSKADYTCR VFGGVYPFMW GGAQCFCDSE N TQLSEAYV ...String:
RPTNAETFGE TLNHLWFNNQ PFLWAQLCIP LAALVILFRC FSCCMPFLLV AGVCLGKVDA FEHATTVPNV PGIPYKALVE RAGYAPLNL EITVVSSELT PSTNKEYVTC RFHTVIPSPQ VKCCGSLECK ASSKADYTCR VFGGVYPFMW GGAQCFCDSE N TQLSEAYV EFAPDCTIDH AVALKVHTAA LKVGLRIVYG NTTAHLDTFV NGVTPGSSRD LKVIAGPISA AFSPFDHKVV IR KGLVYNY DFPEYGAMKP GAFGDIQASS LDATDIVART DIRLLKPSVK NIHVPYTQAV SGYEMWKNNS GRPLQETAPF GCK IEVEPL RASNCAYGHI PISIDIPDAA FVRSSESPTI LEVSCTVADC IYSADFGGSL TLQYKADREG HCPVHSHSTT AVLK EATTH VTAVGSITLH FSTSSPQANF IVSLCGKKTT CNAECKPPAD HIIGEPHKVD QEFQAAVSKT SWNWLLALFG GASSL IVVG LIVLV

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Macromolecule #3: Antibody Fab SKT05 heavy chain

MacromoleculeName: Antibody Fab SKT05 heavy chain / type: protein_or_peptide / ID: 3 / 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 #4: Antibody Fab SKT05 light chain

MacromoleculeName: Antibody Fab SKT05 light chain / type: protein_or_peptide / ID: 4 / 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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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4109460
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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