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- EMDB-61503: Rat hepatitis E virus capsid protein E2s domain in complex with Fab C6 -

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Basic information

Entry
Database: EMDB / ID: EMD-61503
TitleRat hepatitis E virus capsid protein E2s domain in complex with Fab C6
Map data
Sample
  • Complex: Rat HEV capsid protein E2s domain in complex with Fab C6
    • Complex: Rat HEV E2s domain
      • Protein or peptide: Pro-secreted protein ORF2
    • Complex: C6 Fab
      • Protein or peptide: C6 Fab heavy chain
      • Protein or peptide: C6 Fab light chain
KeywordsHepatitis E virus / Capsid protein / E2s domain / Immune complex / C6 antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell surface / host cell Golgi apparatus / structural molecule activity / RNA binding / extracellular region
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Viral coat protein subunit
Similarity search - Domain/homology
Pro-secreted protein ORF2
Similarity search - Component
Biological speciesRocahepevirus ratti / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsLiu L / Zheng Q / Li S / Xia N
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: J Hepatol / Year: 2025
Title: Antibodies elicited by hepatitis E vaccination in humans confer cross-genus protection against rat hepatitis E virus.
Authors: Zihao Chen / Liqin Liu / Jianwen Situ / Guanghui Li / Shaoqi Guo / Qi Lai / Shusheng Wu / Yanan Jiang / Jingyan Fan / Zimin Tang / Yu Li / Guiping Wen / Siling Wang / Dong Ying / Yonghao ...Authors: Zihao Chen / Liqin Liu / Jianwen Situ / Guanghui Li / Shaoqi Guo / Qi Lai / Shusheng Wu / Yanan Jiang / Jingyan Fan / Zimin Tang / Yu Li / Guiping Wen / Siling Wang / Dong Ying / Yonghao Liang / Stanley Siu-Fung Ho / Xiaodan Ma / James Yiu-Hung Tsoi / Estie Hon-Kiu Shun / Nicholas Foo-Siong Chew / Weihui Ma / Weiwei Mao / Tingting Li / Zhenqin Chen / Mujin Fang / Yingbin Wang / Hai Yu / Fa Zhang / Anna Jinxia Zhang / Shaowei Li / Ningshao Xia / Siddharth Sridhar / Qingbing Zheng / Zizheng Zheng /
Abstract: BACKGROUND & AIMS: Paslahepevirus balayani (bHEV), also known as hepatitis E virus (HEV), encompasses eight genotypes, five of which infect humans. Rats are natural reservoirs of Rocahepevirus ratti ...BACKGROUND & AIMS: Paslahepevirus balayani (bHEV), also known as hepatitis E virus (HEV), encompasses eight genotypes, five of which infect humans. Rats are natural reservoirs of Rocahepevirus ratti genotype 1 (HEV-r-1; rat HEV; rHEV), which has recently been implicated in viral hepatitis. Despite the antigenic divergence between bHEV and rHEV, studies on shared protective antibodies remain rare.
METHODS: Polyclonal and monoclonal antibody responses against bHEV and rHEV were analyzed using antibody enzyme-linked immunosorbent assays. The efficacy of six potent bHEV-elicited cross-reactive ...METHODS: Polyclonal and monoclonal antibody responses against bHEV and rHEV were analyzed using antibody enzyme-linked immunosorbent assays. The efficacy of six potent bHEV-elicited cross-reactive antibodies in preventing rHEV infection was evaluated via challenge assays in rats. Cryo-electron microscopy was performed to assess the structural basis for the differential protective efficacy of the six antibodies. The viral lysis ability of these antibodies was assessed by separately reacting purified HEV-b-1 and HEV-r-1 virions with each antibody.
RESULTS: We determined that antibody responses to bHEV infection and vaccination possess limited cross-reactivity to rHEV and identified two cross-reactive antigenic sites within the E2s domain. ...RESULTS: We determined that antibody responses to bHEV infection and vaccination possess limited cross-reactivity to rHEV and identified two cross-reactive antigenic sites within the E2s domain. Structural analysis and animal challenge studies pinpointed potent cross-reactive antibodies targeting antigenic site 1, indicating its prophylactic efficacy against rHEV. Conversely, antibodies recognizing antigenic site 2 were found to facilitate viral lysis of bHEV but not rHEV.
CONCLUSIONS: These findings underscore the importance of antigenic site 1 in the design of broad-spectrum vaccines and therapeutics to mitigate the impact of diverse HEV genotypes on human health.
IMPACT AND IMPLICATIONS: Rat HEV (rHEV) spillover to humans represents an unprecedented threat. Significant antigenic differences between rHEV and bHEV (Paslahepevirus balayani) may exacerbate the ...IMPACT AND IMPLICATIONS: Rat HEV (rHEV) spillover to humans represents an unprecedented threat. Significant antigenic differences between rHEV and bHEV (Paslahepevirus balayani) may exacerbate the impact of viral hepatitis. Our study reveals that cross-reactive human antibodies can offer protection against rHEV infection. Cross-protective antibodies targeting antigenic site 1 can be used to guide the development of practical strategies for preventing rHEV infection.
History
DepositionSep 11, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61503.png

Downloads & links

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Map

FileDownload / File: emd_61503.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.044635274 - 2.182447
Average (Standard dev.)0.0008606928 (±0.019057168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61503_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_61503_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rat HEV capsid protein E2s domain in complex with Fab C6

EntireName: Rat HEV capsid protein E2s domain in complex with Fab C6
Components
  • Complex: Rat HEV capsid protein E2s domain in complex with Fab C6
    • Complex: Rat HEV E2s domain
      • Protein or peptide: Pro-secreted protein ORF2
    • Complex: C6 Fab
      • Protein or peptide: C6 Fab heavy chain
      • Protein or peptide: C6 Fab light chain

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Supramolecule #1: Rat HEV capsid protein E2s domain in complex with Fab C6

SupramoleculeName: Rat HEV capsid protein E2s domain in complex with Fab C6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rocahepevirus ratti

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Supramolecule #2: Rat HEV E2s domain

SupramoleculeName: Rat HEV E2s domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rocahepevirus ratti

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Supramolecule #3: C6 Fab

SupramoleculeName: C6 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pro-secreted protein ORF2

MacromoleculeName: Pro-secreted protein ORF2 / type: protein_or_peptide / ID: 1
Details: Sequence reference for source organism Rocahepevirus ratti is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3G1TVH2.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rocahepevirus ratti
Molecular weightTheoretical: 16.604471 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
APARPITNWR SGDVVWVTLP SAEYAQSQSA MGSHPAYWSE EATIINVATG QRAAVSSIKW DQVTLNGKAL HKETHSGLVY YQLPLMGKI NFWQQGTTKA GYTYNYNTTD SDSLWVWWDG GSKAYLYIST YTTMLGAGPV NITGLGAVGP NPV

UniProtKB: Pro-secreted protein ORF2

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Macromolecule #2: C6 Fab heavy chain

MacromoleculeName: C6 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.60716 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFR SYAIHWVRQA PGKGLEWVAL ISYDGSNGYY ADSVKGRFTI SRDNSKNTVY LQVNTLRAE DTALYYCARD RGSIVEPAAL YIDYWGQGTL VTVSS

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Macromolecule #3: C6 Fab light chain

MacromoleculeName: C6 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.425632 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SAAPGQMVTI SCSGSSSNIG NNYVSWYQHL PGTAPKLLIY DNNKRPSGIP DRFSGSKSGT SVTLGITGLQ TGDEADYYC GTWDSSLSAV VFGGGTKLTV L

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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 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145143
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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