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- EMDB-50610: Cryo-EM structure of the P domain of the Hepatitis E Virus ORF2 p... -

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Basic information

Entry
Database: EMDB / ID: EMD-50610
TitleCryo-EM structure of the P domain of the Hepatitis E Virus ORF2 protein in complex with Fab ES4.431
Map data
Sample
  • Complex: Complex of Hepatitis Virus ORF2 protein with the Fab fragment of the neutralizing antibody ES1.327
    • Protein or peptide: Secreted protein ORF2
    • Protein or peptide: Human IgG antibody Es4.431 -Fab heavy chain
    • Protein or peptide: Human IgG antibody Es4.431 - Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHepatitis E / capsid protein / viral entry / neutralizing antibody / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell Golgi apparatus / host cell surface / host cell nucleus / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBaquero E / Molinos L / Mouquet H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for the neutralization of Hepatitis E virus by human monoclonal antibodies
Authors: Molinos L / Baquero E / Mouquet H
History
DepositionJun 11, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50610.png

Downloads & links

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Map

FileDownload / File: emd_50610.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.8844596 - 1.6529077
Average (Standard dev.)0.00007110652 (±0.035175398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50610_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50610_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 : Complex of Hepatitis Virus ORF2 protein with the Fab fragment of ...

EntireName: Complex of Hepatitis Virus ORF2 protein with the Fab fragment of the neutralizing antibody ES1.327
Components
  • Complex: Complex of Hepatitis Virus ORF2 protein with the Fab fragment of the neutralizing antibody ES1.327
    • Protein or peptide: Secreted protein ORF2
    • Protein or peptide: Human IgG antibody Es4.431 -Fab heavy chain
    • Protein or peptide: Human IgG antibody Es4.431 - Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Hepatitis Virus ORF2 protein with the Fab fragment of ...

SupramoleculeName: Complex of Hepatitis Virus ORF2 protein with the Fab fragment of the neutralizing antibody ES1.327
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Secreted protein ORF2

MacromoleculeName: Secreted protein ORF2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.886715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSRGAILRRQ YNLSTSPLTS SVASGTNLVL YAAPLNPLLP LQDGTNTHIM ATEASNYAQY RVVRATIRYR PLVPNAVGGY AISISFWPQ TTTTPTSVDM NSITSTDVRI LVQPGIASEL VIPSERLHYR NQGWRSVETT GVAEEEATSG LVMLCIHGSP V NSYTNTPY ...String:
DSRGAILRRQ YNLSTSPLTS SVASGTNLVL YAAPLNPLLP LQDGTNTHIM ATEASNYAQY RVVRATIRYR PLVPNAVGGY AISISFWPQ TTTTPTSVDM NSITSTDVRI LVQPGIASEL VIPSERLHYR NQGWRSVETT GVAEEEATSG LVMLCIHGSP V NSYTNTPY TGALGLLDFA LELEFRNLTP GNTNTRVSRY TSTARHRLRR GADGTAELTT TAATRFMKDL HFTGTNGVGE VG RGIALTL FNLADTLLGG LPTELISSAG GQLFYSRPVV SANGEPTVKL YTSVENAQQD KGITIPHDID LGDSRVVIQD YDN QHEQDR PTPSPAPSRP FSVLRANDVL WLSLTAAEYD QTTYGSSTNP MYVSDTVTFV NVATGAQAVA RSLDWSKVTL DGRP LTTIQ QYSKTFYVLP LRGKLSFWEA STTKAGYPYN YNTTASDQIL IENAAGHRVA ISTYTTSLGA GPTSISAVGV LHHHH HHHH HH

UniProtKB: Pro-secreted protein ORF2

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Macromolecule #2: Human IgG antibody Es4.431 -Fab heavy chain

MacromoleculeName: Human IgG antibody Es4.431 -Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.087059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGGSLRL SCTASGFTFD THVMSWVRQG PGKGLEWVSS ISAASGTYYA GSVKGRFTIS RDNSKNTLFL HMNSLRVED TGVYYCANVV HRCTTNTCFR GADNWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLLESGGG LVQPGGSLRL SCTASGFTFD THVMSWVRQG PGKGLEWVSS ISAASGTYYA GSVKGRFTIS RDNSKNTLFL HMNSLRVED TGVYYCANVV HRCTTNTCFR GADNWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTHHHHHH

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Macromolecule #3: Human IgG antibody Es4.431 - Fab light chain

MacromoleculeName: Human IgG antibody Es4.431 - Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.779246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PSSLSASVGD RVTITCRASQ SVDTYLNWYQ QKPGETPKLL IYAASTLQSG VPSRFSGSGS GTTFTLTISS LQPEDFATYY CQQSYTTLM YTFGQGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS ...String:
PSSLSASVGD RVTITCRASQ SVDTYLNWYQ QKPGETPKLL IYAASTLQSG VPSRFSGSGS GTTFTLTISS LQPEDFATYY CQQSYTTLM YTFGQGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / 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 / Details: PBS buffer
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ztn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106903
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9fnt:
Cryo-EM structure of the P domain of the Hepatitis E Virus ORF2 protein in complex with Fab ES4.431

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