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- EMDB-43980: Cryo-EM structure of SINV/EEEV in complex with a potently neutral... -

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Basic information

Entry
Database: EMDB / ID: EMD-43980
TitleCryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373
Map data
Sample
  • Complex: EEEV in complex with IgG EEEV-373
    • Protein or peptide: IgG EEEV-373 Heavy chain
    • Protein or peptide: IgG EEEV-373 Light chain
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: E2 glycoprotein
  • Ligand: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscryo-EM / single particle / virus neutralization / intra-virion crosslink / VIRUS-IMMUNE SYSTEM complex / VIRUS
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-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / 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
E2 glycoprotein / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsBandyopadhyay A / Klose T / Kuhn RJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI095366 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373
Authors: Bandyopadhyay A / Klose T / Kuh RJ
History
DepositionMar 7, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43980.png

Downloads & links

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Map

FileDownload / File: emd_43980.map.gz / Format: CCP4 / Size: 963 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 632 pix.
= 1193.216 Å		1.89 Å/pix.
x 632 pix.
= 1193.216 Å		1.89 Å/pix.
x 632 pix.
= 1193.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.888 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-24.838418999999998 - 38.561503999999999
Average (Standard dev.)0.16359131 (±2.7318692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-316-316-316
Dimensions632632632
Spacing632632632
CellA=B=C: 1193.2161 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43980_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_43980_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 : EEEV in complex with IgG EEEV-373

EntireName: EEEV in complex with IgG EEEV-373
Components
  • Complex: EEEV in complex with IgG EEEV-373
    • Protein or peptide: IgG EEEV-373 Heavy chain
    • Protein or peptide: IgG EEEV-373 Light chain
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: E2 glycoprotein
  • Ligand: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: EEEV in complex with IgG EEEV-373

SupramoleculeName: EEEV in complex with IgG EEEV-373 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL93-939

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Macromolecule #1: IgG EEEV-373 Heavy chain

MacromoleculeName: IgG EEEV-373 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.386211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SHVMYWVRQA PGKGLEWVAV ITYDGGNKYY ADSVRGRLTI SRDNSKNTLY LQMNSLRAE DTAVYYCASP RGDSGSYYDI DYFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SHVMYWVRQA PGKGLEWVAV ITYDGGNKYY ADSVRGRLTI SRDNSKNTLY LQMNSLRAE DTAVYYCASP RGDSGSYYDI DYFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC

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Macromolecule #2: IgG EEEV-373 Light chain

MacromoleculeName: IgG EEEV-373 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.296922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSA MSASVGDRVT ITCRASQGIS NYLAWFQQKP GKVPKRLIYA ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCL QHNTSPSPFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSA MSASVGDRVT ITCRASQGIS NYLAWFQQKP GKVPKRLIYA ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCL QHNTSPSPFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKLYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL 93-939
Molecular weightTheoretical: 43.628023 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FTGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String:
YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FTGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS SAWSPFDNKV VVYGHEVYNY DFPEYGTGKA GSFGDLQSRT STSNDLYANT NLKLQRPQAG IVHTPFTQAP SG FERWKRD KGAPLNDVAP FGCSIALEPL RAENCAVGSI PISIDIPDAA FTRISETPTV SDLECKITEC TYASDFGGIA TVA YKSSKA GNCPIHSPSG VAVIKENDVT LAESGSFTFH FSTANIHPAF KLQVCTSAVT CKGDCKPPKD HIVDYPAQHT ESFT

UniProtKB: Structural polyprotein

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Macromolecule #4: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL 93-939
Molecular weightTheoretical: 37.921133 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ ...String:
DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ PGLVADHSLL SIHSAKVKIT VPSGAQVKYY CKCPDVREGI TSSDHTTTCT DVKQCRAYLI DNKKWVYNSG RL PRGEGDT FKGKLHVPFV PVKAKCIATL APEPLVEHKH RTLILHLHPD HPTLLTTRSL GSDANPTRQW IERPTTVNFT VTG EGLEYT WGNHPPKRVW AQ

UniProtKB: E2 glycoprotein

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Macromolecule #7: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 4 / 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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.49 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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: 17830
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 15932
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: jspr
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6mx4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ay1:
Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373

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