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- EMDB-61509: Rat hepatitis E virus capsid protein E2s domain in complex with F... -

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Basic information

Entry
Database: EMDB / ID: EMD-61509
TitleRat hepatitis E virus capsid protein E2s domain in complex with Fab C131
Map data
Sample
  • Complex: Rat HEV capsid protein E2s domain in complex with Fab C131
    • Complex: Rat HEV E2s domain
      • Protein or peptide: Pro-secreted protein ORF2
    • Complex: C131 Fab
      • Protein or peptide: C131 Fab heavy chain
      • Protein or peptide: C131 Fab light chain
KeywordsHepatitis E virus / Capsid protein / E2s domain / Immune complex / C131 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 Golgi apparatus / host cell surface / 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: 2.44 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-EM 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. ...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: rHEV spillover to humans represents an unprecedented threat. Significant antigenic differences between rHEV and bHEV 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 inform the development of practical strategies for preventing rHEV infection.
History
DepositionSep 12, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61509.png

Downloads & links

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Map

FileDownload / File: emd_61509.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 0.1
Minimum - Maximum-0.083379604 - 2.0025854
Average (Standard dev.)0.00093975157 (±0.020886492)
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_61509_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61509_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 C131

EntireName: Rat HEV capsid protein E2s domain in complex with Fab C131
Components
  • Complex: Rat HEV capsid protein E2s domain in complex with Fab C131
    • Complex: Rat HEV E2s domain
      • Protein or peptide: Pro-secreted protein ORF2
    • Complex: C131 Fab
      • Protein or peptide: C131 Fab heavy chain
      • Protein or peptide: C131 Fab light chain

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Supramolecule #1: Rat HEV capsid protein E2s domain in complex with Fab C131

SupramoleculeName: Rat HEV capsid protein E2s domain in complex with Fab C131
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: C131 Fab

SupramoleculeName: C131 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 / 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: C131 Fab heavy chain

MacromoleculeName: C131 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.670113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKTSGGTFS TYGISWVRQA PGQGLEWLGG IIPIFATPNY AQNFQGRLTI TADESTSTAY MELTSLRSD DTAVYYCARE AQPNPWFREN NRFDPWGQGT LVTVSS

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Macromolecule #3: C131 Fab light chain

MacromoleculeName: C131 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.45857 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTSSDVG SYDLVSWYQQ QPGKAPKLII YEGNKRPSGV SHRFSGSNSG NTASLTISGL QAEDEADYY CCSFAISVTF VFGTGTKVTV 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: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68077
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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