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- PDB-8pmy: HEV gt3 P domain in complex with glycan-insensitive nAb p60.15 -

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Basic information

Entry
Database: PDB / ID: 8pmy
TitleHEV gt3 P domain in complex with glycan-insensitive nAb p60.15
Components
  • Capsid protein
  • scFv_p60.15
KeywordsVIRAL PROTEIN / HEV / P domain / non-glycosylated / glycan-insensitive / neutralizing antibody (nAb)
Function / homology: / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / viral capsid / metal ion binding / Capsid protein
Function and homology information
Biological speciesHomo sapiens (human)
Paslahepevirus balayani
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsSsebyatika, G. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation9A888 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Broadly neutralizing antibodies isolated from HEV convalescents confer protective effects in human liver-chimeric mice.
Authors: Ssebyatika, G. / Dinkelborg, K. / Stroh, L.J. / Hinte, F. / Corneillie, L. / Hueffner, L. / Guzman, E.M. / Nankya, P.L. / Pluckebaum, N. / Fehlau, L. / Garn, J. / Meyer, N. / Prallet, S. / ...Authors: Ssebyatika, G. / Dinkelborg, K. / Stroh, L.J. / Hinte, F. / Corneillie, L. / Hueffner, L. / Guzman, E.M. / Nankya, P.L. / Pluckebaum, N. / Fehlau, L. / Garn, J. / Meyer, N. / Prallet, S. / Mehnert, A.K. / Kraft, A.R.M. / Verhoye, L. / Jacobsen, C. / Steinmann, E. / Wedemeyer, H. / Viejo-Borbolla, A. / Dao Thi, V.L. / Pietschmann, T. / Lutgehetmann, M. / Meuleman, P. / Dandri, M. / Krey, T. / Behrendt, P.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv_p60.15
B: Capsid protein
L: scFv_p60.15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3976
Polymers77,2013
Non-polymers1963
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-83 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.19, 122.95, 158.67
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody scFv_p60.15


Mass: 27166.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly)
#2: Protein Capsid protein


Mass: 22868.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paslahepevirus balayani / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A6C0PR31
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 11% w/v PEG 8000, 0.1M Zinc acetate and 0.1M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.406→48.64 Å / Num. obs: 21742 / % possible obs: 99.61 % / Redundancy: 13.12 % / CC1/2: 0.993 / Rrim(I) all: 0.293 / Net I/σ(I): 7.43
Reflection shellResolution: 2.406→2.492 Å / Num. unique obs: 2122 / CC1/2: 0.482

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→48.65 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1087 -RANDOM
Rwork0.2116 ---
obs0.2135 21738 99.8 %-
Displacement parametersBiso mean: 58.19 Å2
Baniso -1Baniso -2Baniso -3
1--13.468 Å20 Å20 Å2
2--24.3157 Å20 Å2
3----10.8477 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.406→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 3 107 2998
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964036HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d964SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes491HARMONIC5
X-RAY DIFFRACTIONt_it2962HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion395SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2507SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.21
LS refinement shellResolution: 2.41→2.42 Å
RfactorNum. reflection% reflection
Rfree0.3985 21 -
Rwork0.3363 --
obs0.3393 435 98.13 %

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