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- EMDB-50643: HEV ORF2 protein in complex with Fabs Es1.114 and Es5.127 -

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Basic information

Entry
Database: EMDB / ID: EMD-50643
TitleHEV ORF2 protein in complex with Fabs Es1.114 and Es5.127
Map data
Sample
  • Complex: Ternary complex of the HEV ORF2 protein with the Fab fragments of the monoclonal antibodies Es5.127 and Es1.114
    • Protein or peptide: Secreted protein ORF2
    • Protein or peptide: human IgG antibody Es5.127 - Fab heavy chain
    • Protein or peptide: Human IgG antibody Es5.127 - Fab light chain
    • Protein or peptide: Human IgG antibody Es1.114 - Fab heavy chain
    • Protein or peptide: Himan IgG antibody Es1.114 - Fab light chain
KeywordsHepatitis E virus / 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) / Hepatitis E virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBaquero E / Molinos L / Mouquet H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HEV ORF2 protein in complex with Fabs Es1.114 and Es5.127
Authors: Molinos L / Baquero E / Mouquet H
History
DepositionJun 14, 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_50643.png

Downloads & links

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Map

FileDownload / File: emd_50643.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. 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: 0.3
Minimum - Maximum-1.6274306 - 2.4130654
Average (Standard dev.)-0.00002465632 (±0.057222318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50643_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_50643_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 : Ternary complex of the HEV ORF2 protein with the Fab fragments of...

EntireName: Ternary complex of the HEV ORF2 protein with the Fab fragments of the monoclonal antibodies Es5.127 and Es1.114
Components
  • Complex: Ternary complex of the HEV ORF2 protein with the Fab fragments of the monoclonal antibodies Es5.127 and Es1.114
    • Protein or peptide: Secreted protein ORF2
    • Protein or peptide: human IgG antibody Es5.127 - Fab heavy chain
    • Protein or peptide: Human IgG antibody Es5.127 - Fab light chain
    • Protein or peptide: Human IgG antibody Es1.114 - Fab heavy chain
    • Protein or peptide: Himan IgG antibody Es1.114 - Fab light chain

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Supramolecule #1: Ternary complex of the HEV ORF2 protein with the Fab fragments of...

SupramoleculeName: Ternary complex of the HEV ORF2 protein with the Fab fragments of the monoclonal antibodies Es5.127 and Es1.114
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Hepatitis E virus
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 Es5.127 - Fab heavy chain

MacromoleculeName: human IgG antibody Es5.127 - Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.675801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGESLKI SCKGSGYRSG YSFSSYWIGW VRQRPGKGLE WMGIIQPGDS DTTYSPSFQG QVTISADKSI NTAYLQWSS LKASDTAIYY CARVRGSLKV PAAVPFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
EVQLVQSGAE VKKPGESLKI SCKGSGYRSG YSFSSYWIGW VRQRPGKGLE WMGIIQPGDS DTTYSPSFQG QVTISADKSI NTAYLQWSS LKASDTAIYY CARVRGSLKV PAAVPFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDKTHHHH HH

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Macromolecule #3: Human IgG antibody Es5.127 - Fab light chain

MacromoleculeName: Human IgG antibody Es5.127 - Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.76216 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NNYVSWYQQF PGIAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYC GTWDSSLSDV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NNYVSWYQQF PGIAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYC GTWDSSLSDV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #4: Human IgG antibody Es1.114 - Fab heavy chain

MacromoleculeName: Human IgG antibody Es1.114 - Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.4564 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVESGGGL VKPGGSLRLS CAASGFIFSD YYLSWIRQAP GKGLEWIAYI SSGGSTIYYA GSVKGRFTIS RDDARNSLYL QMNSLRVED TAVYYCAREP TYHDFGSGYY TGFDYWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
VQLVESGGGL VKPGGSLRLS CAASGFIFSD YYLSWIRQAP GKGLEWIAYI SSGGSTIYYA GSVKGRFTIS RDDARNSLYL QMNSLRVED TAVYYCAREP TYHDFGSGYY TGFDYWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKTHHHHHH

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Macromolecule #5: Himan IgG antibody Es1.114 - Fab light chain

MacromoleculeName: Himan IgG antibody Es1.114 - Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.466975 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PSSLSASIGD RVTITCRASQ SVSVYLNWYQ QKPGKVPKLL IYAASSLQSG VPSRFSGSGS GTDFTLTISS LQPEDFATYY CQQSYNLFT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS ...String:
PSSLSASIGD RVTITCRASQ SVSVYLNWYQ QKPGKVPKLL IYAASSLQSG VPSRFSGSGS GTDFTLTISS LQPEDFATYY CQQSYNLFT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207869
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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