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- EMDB-72748: Localized reconstruction of the asymmetric unit of the low pH tre... -

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Basic information

Entry
Database: EMDB / ID: EMD-72748
TitleLocalized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV.
Map data
Sample
  • Virus: Eastern equine encephalitis virus
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: Capsid protein
    • Protein or peptide: E2 glycoprotein
  • Protein or peptide: E2 glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEastern Equine Encephalitis Virus / Cryo-EM / Single Particle Averaging / localized reconstruction / asymmetric unit / low pH back neutralization. / VIRUS
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / host cell nucleus / virion membrane / structural molecule activity ...T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / host cell nucleus / virion membrane / structural molecule activity / proteolysis / RNA binding
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 / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBandyopadhyay A / Klose T / Kuhn RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI095366 United States
CitationJournal: Nat Commun / Year: 2026
Title: Asymmetric structural transitions in the icosahedral organization of Eastern equine encephalitis virus.
Authors: Abhishek Bandyopadhyay / Lauren E Williamson / Cameron D Buchman / Thomas Klose / James E Crowe / Richard J Kuhn /
Abstract: Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This ...Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This process requires significant structural changes in the alphavirus glycoprotein organization. Structural characterization of acidic pH-induced conformational changes in alphavirus virions has remained elusive due to the rapid, transient nature of these states, conformational heterogeneity, and particle aggregation. Antibody binding studies conducted at elevated temperatures or under acidic pH conditions have further revealed the presence of transitional epitopes that are inaccessible on alphaviruses at room temperature or neutral pH. In this report, we present structural snapshots of the conformational changes in the glycoproteins and nucleocapsid core of a prototypical alphavirus, Eastern equine encephalitis virus, caused by exposure to 40 °C or pH 5.6. These findings provide insights into the structural transitions that occur prior to viral fusion with the endosomal membrane. This approach has also allowed us to define the molecular basis for recognition of a pan-alphavirus epitope by a patient-derived human antibody.
History
DepositionSep 16, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72748.png

Downloads & links

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Map

FileDownload / File: emd_72748.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 210 pix.
= 279.3 Å		1.33 Å/pix.
x 210 pix.
= 279.3 Å		1.33 Å/pix.
x 210 pix.
= 279.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.35160187 - 0.7158138
Average (Standard dev.)0.012234229 (±0.047056235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 279.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_72748_additional_1.map
Projections & Slices
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Additional map: #2

Fileemd_72748_additional_2.map
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Additional map: #1

Fileemd_72748_additional_3.map
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Half map: #2

Fileemd_72748_half_map_1.map
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Half map: #1

Fileemd_72748_half_map_2.map
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Sample components

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Entire : Eastern equine encephalitis virus

EntireName: Eastern equine encephalitis virus
Components
  • Virus: Eastern equine encephalitis virus
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: Capsid protein
    • Protein or peptide: E2 glycoprotein
  • Protein or peptide: E2 glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Culiseta melanura (mosquito)

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus / Strain: Fl 93-939
Molecular weightTheoretical: 47.938141 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 SAISA TAWSWLKVLV GGTSAFIVLG LIATAVVALV LFFHRH

UniProtKB: Structural polyprotein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL 93-939
Molecular weightTheoretical: 17.650041 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString:
QRMCMKLESD KTFPIMLNGQ VNGYACVVGG RVFKPLHVEG RIDNEQLAAI KLKKASIYDL EYGDVPQCMK SDTLQYTSDK PPGFYNWHH GAVQYENNRF TVPRGVGGKG DSGRPILDNK GRVVAIVLGG VNEGSRTALS VVTWNQKGVT VKDTPEGSEP W

UniProtKB: Structural polyprotein

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Macromolecule #3: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL 93-939
Molecular weightTheoretical: 46.860785 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: LDTHFTQYKL ARPYIADCPN CGHSRCDSPI AIEEVRGDAH AGVIRIQTSA MFGLKTDGVD LAYMSFMNGK TQKSIKIDNL HVRTSAPCS LVSHHGYYIL AQCPPGDTVT VGFHDGPNRH TCTVAHKVEF RPVGREKYRH PPEHGVELPC NRYTHKRADQ G HYVEMHQP ...String:
LDTHFTQYKL ARPYIADCPN CGHSRCDSPI AIEEVRGDAH AGVIRIQTSA MFGLKTDGVD LAYMSFMNGK TQKSIKIDNL HVRTSAPCS LVSHHGYYIL AQCPPGDTVT VGFHDGPNRH TCTVAHKVEF RPVGREKYRH PPEHGVELPC NRYTHKRADQ G HYVEMHQP GLVADHSLLS IHSAKVKITV PSGAQVKYYC KCPDVREGIT SSDHTTTCTD VKQCRAYLID NKKWVYNSGR LP RGEGDTF KGKLHVPFVP VKAKCIATLA PEPLVEHKHR TLILHLHPDH PTLLTTRSLG SDANPTRQWI ERPTTVNFTV TGE GLEYTW GNHPPKRVWA QESGEGNPHG WPHEVVVYYY NRYPLTTIIG LCTCVAIIMV SCVTSVWLLC RTRNLCITPY KLAP NAQVP ILLALLCCIK PTR

UniProtKB: E2 glycoprotein

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Macromolecule #4: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: FL 93-939
Molecular weightTheoretical: 46.975875 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 AQESGEGNPH GWPHEVVVYY YNRYPLTTII GLCTCVAIIM VSCVTSVWLL CRTRNLCITP YKLA PNAQV PILLALLCCI KPTR

UniProtKB: E2 glycoprotein

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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: 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: 7.8
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS 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: 36.2 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: 0.6 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 958879
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
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: OTHER
Output model

PDB-9yb4:
Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV.

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