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

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Basic information

Entry
Database: PDB / ID: 8pmx
Titlerat HEV P domain in complex with glycan-sensitive nAb p60.12
Components
  • Fab p60.12-HC
  • Fab p60.12-LC
  • Pro-secreted protein ORF2
KeywordsVIRAL PROTEIN / rat HEV / P domain / non-glycosylated / glycan-sensitive / neutralizing antibody (nAb)
Function / homology
Function and homology information


T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / structural molecule activity / cell surface / 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 speciesHepatitis E virus rat/R63/DEU/2009
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.922 Å
AuthorsSsebyatika, G. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen Foundation9A888 Germany
CitationJournal: To Be Published
Title: A novel class of broadly neutralizing hepatitis E virus-specific human antibodies
Authors: Ssebyatika, G. / Dinkelborg, K. / Stroeh, L.J. / Hinte, F. / Corneillie, L. / Hueffner, L. / Guzman, E.M. / Nankya, P.L. / Plueckebaum, N. / Prallet, S. / Mehnert, A.K. / Verhoye, L. / ...Authors: Ssebyatika, G. / Dinkelborg, K. / Stroeh, L.J. / Hinte, F. / Corneillie, L. / Hueffner, L. / Guzman, E.M. / Nankya, P.L. / Plueckebaum, N. / Prallet, S. / Mehnert, A.K. / Verhoye, L. / Juergens, C. / Steinmann, E. / Wedemeyer, H. / Viejo-Borbolla, A. / Dao Thi, L.V. / Pietschmann, T. / Luetgehetmann, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pro-secreted protein ORF2
B: Pro-secreted protein ORF2
H: Fab p60.12-HC
L: Fab p60.12-LC


Theoretical massNumber of molelcules
Total (without water)83,7264
Polymers83,7264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-46 kcal/mol
Surface area33020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.856, 112.856, 184.439
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pro-secreted protein ORF2 / pORF2 / Protein ORF2


Mass: 17981.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus rat/R63/DEU/2009 / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: E0XL23
#2: Antibody Fab p60.12-HC


Mass: 24858.822 Da / Num. of mol.: 1
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: Antibody Fab p60.12-LC


Mass: 22903.221 Da / Num. of mol.: 1
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)
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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.2M di-Ammonium hydrogen phospahate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.89→48.68 Å / Num. obs: 20832 / % possible obs: 99.6 % / Redundancy: 14.23 % / CC1/2: 0.998 / Rrim(I) all: 0.322 / Net I/σ(I): 7.68
Reflection shellResolution: 3.89→4.13 Å / Num. unique obs: 3268 / CC1/2: 0.401

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.922→48.68 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.792 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.993
RfactorNum. reflection% reflectionSelection details
Rfree0.3615 562 -RANDOM
Rwork0.3 ---
obs0.3038 11444 99.8 %-
Displacement parametersBiso mean: 196.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.0162 Å20 Å20 Å2
2--0.0162 Å20 Å2
3----0.0324 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: LAST / Resolution: 3.922→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5571 0 0 0 5571
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075726HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.867834HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1821SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes939HARMONIC5
X-RAY DIFFRACTIONt_it5726HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion772SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4044SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion20.49
LS refinement shellResolution: 3.922→3.97 Å
RfactorNum. reflection% reflection
Rfree0.4738 20 -
Rwork0.363 --
obs--96.54 %
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)
10-2.9104-2.910402.91040-0.1435-0.54420.5442-0.5442-0.109-0.54420.5442-0.54420.2525-0.08390.1520.1520.17240.07670.30431.8787-41.7857-49.184
21.88832.9104-2.91047.53181.78331.0890.162-0.40960.5442-0.40960.2202-0.54420.5442-0.5442-0.38220.304-0.0877-0.1231-0.1937-0.00050.30427.6676-40.4511-32.9013
300.1028-2.91048.3154-2.910400.058-0.5442-0.5442-0.54420.42830.5442-0.54420.5442-0.48630.304-0.152-0.022-0.3040.0696-0.072322.9406-49.2329-21.5147
48.31540.56512.91044.55782.910400.17840.54420.54420.5442-0.3277-0.14760.5442-0.14760.14930.19950.152-0.152-0.17670.0220.30430.4619-45.9744-39.2669
502.9104-2.91040-2.6171000.5442-0.54420.5442-0.54420.5442-0.54420.54420.54420.3040.152-0.152-0.304-0.1520.30437.2113-52.1525-27.0424
60-2.9104-2.910400.71071.68120.25570.54420.54420.5442-0.2885-0.40350.5442-0.40350.03280.304-0.152-0.152-0.3040.1520.30428.7224-39.2199-26.4939
702.0718-0.60087.3786-1.87334.44570.17220.27360.26310.2736-0.372-0.4520.2631-0.4520.19980.304-0.152-0.152-0.3040.04970.047725.5138-43.8827-22.3978
80-2.9104-2.60296.4078-0.42324.130900.5442-0.38590.54420.5442-0.0363-0.3859-0.0363-0.54420.27210.152-0.152-0.3040.04180.30429.7602-39.2984-28.6908
98.0248-2.91042.91040-2.910400.06430.5442-0.54420.5442-0.48-0.2043-0.5442-0.20430.41570.11270.152-0.1520.3040.01880.016829.8656-19.1354-47.6637
102.658-2.29782.91041.07632.075900.23440.5442-0.54420.54420.0754-0.0729-0.5442-0.0729-0.30980.2019-0.152-0.1520.06580.10980.169331.5613-22.9598-31.3571
1102.91042.91048.31540.548900.33170.5442-0.54420.5442-0.11920.5442-0.54420.5442-0.21250.304-0.152-0.152-0.304-0.1270.278333.988-16.1931-18.6329
128.31542.91042.91048.31540.20042.33210.24960.5442-0.54420.54420.0450.0415-0.54420.0415-0.29460.0468-0.152-0.152-0.16320.1520.30429.7012-16.5888-37.249
130-2.91042.91040.3791-0.87620-0.12380.53880.54420.53880.4205-0.54420.5442-0.5442-0.29670.3040.14370.0755-0.3040.12630.30421.2885-11.3504-25.4834
140-2.0582-1.61791.32371.01212.87090.33720.1788-0.54420.1788-0.13010.1568-0.54420.1568-0.20710.304-0.0933-0.152-0.3040.11470.30429.6511-25.0377-25.4145
1502.91042.91043.66082.91040.53670.14320.54420.02030.54420.25780.54420.02030.5442-0.4010.304-0.152-0.152-0.3040.1520.249532.1265-20.9394-20.2707
168.31542.9104-0.10273.7663-2.910400.06180.54420.35790.54420.42060.17410.35790.1741-0.48240.06050.152-0.1520.03270.06540.30428.9452-24.645-27.764
1702.9104-2.91044.3868-2.2758.315400.5442-0.2250.54420.5442-0.5442-0.225-0.5442-0.54420.304-0.1520.1520.01560.152-0.3049.0218-46.62986.137
181.26542.9104-2.91048.3154-2.91048.3154-0.25620.41460.54420.41460.0212-0.54420.5442-0.54420.2350.304-0.152-0.0303-0.0340.152-0.30415.7108-44.583322.0618
193.9632.18740.12338.31542.91048.31540.0956-0.1897-0.5442-0.1897-0.44860.2879-0.54420.28790.35310.304-0.152-0.152-0.304-0.0953-0.30431.797-33.335710.7411
208.3154-2.91042.91048.31542.91048.31540.3628-0.0513-0.5442-0.0513-0.18140.5442-0.54420.5442-0.18140.304-0.152-0.1520.3040.1520.30431.5165-45.450538.9694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|454 - 464}A454 - 464
2X-RAY DIFFRACTION2{A|465 - 479}A465 - 479
3X-RAY DIFFRACTION3{A|480 - 500}A480 - 500
4X-RAY DIFFRACTION4{A|501 - 521}A501 - 521
5X-RAY DIFFRACTION5{A|522 - 536}A522 - 536
6X-RAY DIFFRACTION6{A|537 - 550}A537 - 550
7X-RAY DIFFRACTION7{A|551 - 594}A551 - 594
8X-RAY DIFFRACTION8{A|595 - 607}A595 - 607
9X-RAY DIFFRACTION9{B|454 - 464}B454 - 464
10X-RAY DIFFRACTION10{B|465 - 479}B465 - 479
11X-RAY DIFFRACTION11{B|480 - 500}B480 - 500
12X-RAY DIFFRACTION12{B|501 - 521}B501 - 521
13X-RAY DIFFRACTION13{B|522 - 536}B522 - 536
14X-RAY DIFFRACTION14{B|537 - 550}B537 - 550
15X-RAY DIFFRACTION15{B|551 - 594}B551 - 594
16X-RAY DIFFRACTION16{B|595 - 607}B595 - 607
17X-RAY DIFFRACTION17{H|2 - 32}H2 - 32
18X-RAY DIFFRACTION18{H|33 - 224}H33 - 224
19X-RAY DIFFRACTION19{L|3 - 127}L3 - 127
20X-RAY DIFFRACTION20{L|128 - 215}L128 - 215

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