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- EMDB-50742: Cryo-EM recostruction of the complex between Rocahepevirus ratti ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50742
TitleCryo-EM recostruction of the complex between Rocahepevirus ratti (HEV rat) ORF2 protein in complex with Fab of antibody Es5.127
Map data
Sample
  • Complex: Complex of Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of antibody Es5.127
    • Protein or peptide: Rocahepevirus ratti (HEV rat) ORF2 protein
    • Protein or peptide: Antibody Es5.127 - Fab Heavy chain
    • Protein or peptide: Antibody Es5.127 - Fab Light Chain
KeywordsHepatitis E virus / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Rocahepevirus ratti
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBaquero E / Molinos L / Mouquet H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM recostruction of the complex between Rocahepevirus ratti (HEV rat) ORF2 protein in complex with Fab of antibody Es5.127
Authors: Molinos L / Baquero E / Mouquet H
History
DepositionJun 24, 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_50742.png

Downloads & links

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Map

FileDownload / File: emd_50742.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 180 pix.
= 268.2 Å		1.49 Å/pix.
x 180 pix.
= 268.2 Å		1.49 Å/pix.
x 180 pix.
= 268.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1873715 - 1.5988904
Average (Standard dev.)0.0017364477 (±0.03139409)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 268.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50742_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_50742_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 Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of...

EntireName: Complex of Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of antibody Es5.127
Components
  • Complex: Complex of Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of antibody Es5.127
    • Protein or peptide: Rocahepevirus ratti (HEV rat) ORF2 protein
    • Protein or peptide: Antibody Es5.127 - Fab Heavy chain
    • Protein or peptide: Antibody Es5.127 - Fab Light Chain

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Supramolecule #1: Complex of Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of...

SupramoleculeName: Complex of Rocahepevirus ratti (HEV rat) ORF2 protein with Fab of antibody Es5.127
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Rocahepevirus ratti (HEV rat) ORF2 protein

MacromoleculeName: Rocahepevirus ratti (HEV rat) ORF2 protein / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Rocahepevirus ratti
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSRGSILRRQ YNLSTSPLTL TVPQSSNSIL YAASLNPLLP LQDGSNTHIM ATEASNYAQY RVQACTLHFR PLVPNSVGGY AVSMSFWPQS TTVPTSVDMN SITSTDVRIV AQPGLAAELV VPRERLHYRN QGWRSVETNS VPQEESTSGM LMVCIHGAPI NSFTNSAYTG ...String:
DSRGSILRRQ YNLSTSPLTL TVPQSSNSIL YAASLNPLLP LQDGSNTHIM ATEASNYAQY RVQACTLHFR PLVPNSVGGY AVSMSFWPQS TTVPTSVDMN SITSTDVRIV AQPGLAAELV VPRERLHYRN QGWRSVETNS VPQEESTSGM LMVCIHGAPI NSFTNSAYTG ALGLLDIALQ VEYRNLTPGN TNTRVNRFRT TAPHKIKRLP DGTAQVATAS AVRFMQDVHL TGGNGVGDIG KGIVQVLFNI ADTLLGGLPT DLVSNAGGQL FYGRPQVSEN GEPSVKLYTS VEAAQLDQGV TIPHDIDLGL STVTLQDFDN QHLQDRPTPS PAPARPITNW RSGDVVWVTL PSAEYAQSQS AMGSHPAYWS EEATIINVAT GQRALVSSIK WDQVTLNGKV LHKETHSGLV YYQLPLMGKI SFWQQGTTKA GYTYNYNTTD SDSLWVWWDG TSKGYLYVST YTTMLGAGPV NITGLGAIHH HHHHHHHH

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Macromolecule #2: Antibody Es5.127 - Fab Heavy chain

MacromoleculeName: Antibody Es5.127 - Fab Heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGESLKI SCKGSGYRSG YSFSSYWIGW VRQRPGKGLE WMGIIQPGDS DTTYSPSFQG QVTISADKSI NTAYLQWSSL KASDTAIYYC ARVRGSLKVP AAVPFDPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN ...String:
EVQLVQSGAE VKKPGESLKI SCKGSGYRSG YSFSSYWIGW VRQRPGKGLE WMGIIQPGDS DTTYSPSFQG QVTISADKSI NTAYLQWSSL KASDTAIYYC ARVRGSLKVP AAVPFDPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDKTHHHHHH

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Macromolecule #3: Antibody Es5.127 - Fab Light Chain

MacromoleculeName: Antibody Es5.127 - Fab Light Chain / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NNYVSWYQQF PGIAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYCG TWDSSLSDVV FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK ...String:
QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NNYVSWYQQF PGIAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYCG TWDSSLSDVV FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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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
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: PDB ENTRY
PDB model - PDB ID:

9fq3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56650
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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