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- PDB-8pn0: HEV gt3 P domain in complex with glycan-sensitive nAb p60.12 -

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Basic information

Entry
Database: PDB / ID: 8pn0
TitleHEV gt3 P domain in complex with glycan-sensitive nAb p60.12
Components
  • Capsid protein
  • Fab_p60.12-HC
  • Fab_p60.12-LC
KeywordsVIRAL PROTEIN / HEV / P domain / non-glycosylated / glycan-sensitive / 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: 2.072 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 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: Fab_p60.12-HC
B: Fab_p60.12-LC
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
H: Fab_p60.12-HC
L: Fab_p60.12-LC


Theoretical massNumber of molelcules
Total (without water)186,9988
Polymers186,9988
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.43, 94.48, 91.25
Angle α, β, γ (deg.)90, 90.21, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fab_p60.12-HC


Mass: 24858.822 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 S2 cells / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody Fab_p60.12-LC


Mass: 22903.221 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)
#3: Protein
Capsid protein


Mass: 22868.492 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% w/v PEG 4000, 0.2M Calcium chloride and 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 2.072→47.24 Å / Num. obs: 77331 / % possible obs: 84.75 % / Redundancy: 3.27 % / CC1/2: 0.991 / Rrim(I) all: 0.129 / Net I/σ(I): 5.3
Reflection shellResolution: 2.072→2.146 Å / Num. unique obs: 3527 / CC1/2: 0.193

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.072→47.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.288 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.272 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 3868 -RANDOM
Rwork0.2259 ---
obs0.2276 77331 84.8 %-
Displacement parametersBiso mean: 50.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.0643 Å20 Å2-0.0053 Å2
2---4.5545 Å20 Å2
3---3.4902 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.072→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10963 0 0 184 11147
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0115379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3584SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1859HARMONIC5
X-RAY DIFFRACTIONt_it11236HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1560SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8274SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.09
LS refinement shellResolution: 2.072→2.11 Å
RfactorNum. reflection% reflection
Rfree0.3754 78 -
Rwork0.3892 --
obs--31.62 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00810.5781-0.7911.29320.84090.00250.04190.0873-0.38750.0873-0.10570.284-0.38750.2840.0638-0.039-0.05260.02520.03680.0386-0.036527.146621.658721.5126
21.1145-0.33960.32540-0.71590.44020.0868-0.0199-0.0768-0.0199-0.10920.1326-0.07680.13260.0224-0.0115-0.01650.01010.05330.0068-0.069621.868215.584119.0406
30.7598-1.52892.14280-0.96022.1646-0.03860.13010.37230.13010.4188-0.10960.3723-0.1096-0.3802-0.0787-0.08030.03870.28460.1517-0.222153.647110.11593.7651
43.6822-0.653-0.76130-1.05493.15560.04970.35940.23880.35940.23750.15780.23880.1578-0.2872-0.1538-0.0411-0.03240.18050.0637-0.134657.14869.90322.5627
5-0.0038-0.34060.51620-0.59121.65480.20930.10090.22240.1009-0.14280.1860.22240.186-0.0666-0.00120.07030.00430.05560.0034-0.086114.480512.1951-0.6886
60.0037-1.2468-0.501600.21831.03230.36160.0420.22670.042-0.18140.27070.22670.2707-0.1802-0.01370.1511-0.03120.1509-0.0111-0.126225.4689.0938-2.5933
72.3939-0.80071.82180.2143-1.41972.87550.11560.2932-0.22790.29320.3174-0.145-0.2279-0.145-0.4331-0.15920.0685-0.15220.11520.1522-0.092445.5836-0.7304-1.2558
80.91071.95552.913701.72510.0213-0.06560.14320.54410.14320.08590.05090.54410.0509-0.0204-0.07250.1518-0.15240.03050.06270.040348.5678-10.0617-3.8901
90.4095-0.3686-0.01920.4604-0.23780.4822-0.06940.03690.00440.03690.1085-0.07410.0044-0.0741-0.0391-0.00260.01330.01630.02760.1064-0.0515-14.035129.29173.0167
101.03530.1768-0.33740.0963-0.07870.24820.0368-0.0139-0.015-0.01390.0165-0.0237-0.015-0.0237-0.05330.0241-0.00310.0036-0.02910.0495-0.03-10.46315.643523.02
110.12640.3548-0.06320-0.17140.9933-0.1146-0.0120.1605-0.0120.0804-0.16510.1605-0.16510.03420.0316-0.04060.0207-0.02960.008-0.0279-17.1864-28.755542.6005
120.6358-0.02840.10490.2176-0.22460.2334-0.11870.03130.07530.03130.0723-0.0710.0753-0.0710.0464-0.0077-0.04370.01750.02240.0052-0.0414-13.7332-14.858622.7127
131.1150.55860.65040.22420.18720.5453-0.04810.0980.08340.098-0.09330.07910.08340.07910.1414-0.02250.01310.044-0.03210.00090.019422.7362-18.532726.6127
141.05420.1072-0.06861.8324-0.62480.0660.0773-0.00890.085-0.0089-0.0153-0.23920.085-0.2392-0.062-0.01350.00290.05210.0215-0.0005-0.047316.6289-14.971620.6901
150.7755-0.06940.059100.04720.0074-0.0966-0.00330.046-0.00330.05370.08540.0460.08540.0429-0.00150.01370.03020.02210.0155-0.046232.9436-11.841234.4852
160.5440.41840.47840.0392-0.98692.4127-0.14210.03770.0440.03770.1816-0.04780.044-0.0478-0.0395-0.06190.05480.02280.05170.0125-0.044453.187-10.76744.6614
170.61590.22120.77110.2421-0.00121.1111-0.0054-0.0374-0.0459-0.0374-0.0779-0.0503-0.0459-0.05030.08330.00080.02520.013-0.028-0.0125-0.016411.8755-12.099646.0858
180.57930.96780.354300.77780.0026-0.07040.0595-0.2160.05950.01790.147-0.2160.1470.0525-0.00970.020.019-0.0050.0004-0.009814.5542-9.501844.9231
192.0040.85-0.87550.0575-0.5840.72890.06020.11850.05610.1185-0.0114-0.05440.0561-0.0544-0.0488-0.04770.01730.0620.01990.03680.006244.05812.025749.8942
202.59950.9669-2.12370.0069-0.78081.95810.22580.0976-0.05930.09760.0906-0.2403-0.0593-0.2403-0.3164-0.08060.03740.0624-0.03940.06440.020344.0574.1649.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 31}A2 - 31
2X-RAY DIFFRACTION2{A|32 - 121}A32 - 121
3X-RAY DIFFRACTION3{A|122 - 176}A122 - 176
4X-RAY DIFFRACTION4{A|177 - 224}A177 - 222
5X-RAY DIFFRACTION5{B|3 - 76}B3 - 76
6X-RAY DIFFRACTION6{B|77 - 123}B77 - 123
7X-RAY DIFFRACTION7{B|124 - 186}B124 - 186
8X-RAY DIFFRACTION8{B|187 - 216}B187 - 215
9X-RAY DIFFRACTION9{E|459 - 604}E459 - 604
10X-RAY DIFFRACTION10{F|459 - 604}F459 - 604
11X-RAY DIFFRACTION11{C|459 - 604}C459 - 604
12X-RAY DIFFRACTION12{D|459 - 604}D459 - 604
13X-RAY DIFFRACTION13{H|2 - 45}H2 - 45
14X-RAY DIFFRACTION14{H|46 - 83}H46 - 83
15X-RAY DIFFRACTION15{H|84 - 156}H84 - 156
16X-RAY DIFFRACTION16{H|157 - 224}H157 - 224
17X-RAY DIFFRACTION17{L|3 - 68}L3 - 68
18X-RAY DIFFRACTION18{L|69 - 110}L69 - 110
19X-RAY DIFFRACTION19{L|111 - 161}L111 - 161
20X-RAY DIFFRACTION20{L|162 - 216}L162 - 215

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