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- PDB-8pmw: HEV gt3 P domain in complex with glycan-sensitive nAb p60.1 -

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Basic information

Entry
Database: PDB / ID: 8pmw
TitleHEV gt3 P domain in complex with glycan-sensitive nAb p60.1
Components
  • Capsid protein
  • scFv_p60.1
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 / ACETATE ION / Capsid protein
Function and homology information
Biological speciesHomo sapiens (human)
Hepatitis E virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv_p60.1
B: scFv_p60.1
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: scFv_p60.1
H: scFv_p60.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,59514
Polymers198,1678
Non-polymers4286
Water5,549308
1
A: scFv_p60.1
B: scFv_p60.1
C: Capsid protein
E: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2987
Polymers99,0834
Non-polymers2143
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Capsid protein
F: Capsid protein
G: scFv_p60.1
H: scFv_p60.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2987
Polymers99,0834
Non-polymers2143
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.81, 159.26, 205.67
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody
scFv_p60.1


Mass: 26673.227 Da / Num. of mol.: 4
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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A6C0PR31
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.6 / Details: 2M (NH4)2SO4 and 0.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→48.44 Å / Num. obs: 86313 / % possible obs: 99.47 % / Redundancy: 13.23 % / CC1/2: 0.998 / Rrim(I) all: 0.13 / Net I/σ(I): 12.43
Reflection shellResolution: 1.98→2.051 Å / Num. unique obs: 8192 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→48.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 4316 -RANDOM
Rwork0.2063 ---
obs0.2073 86311 99.5 %-
Displacement parametersBiso mean: 45.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.6854 Å20 Å20 Å2
2---6.2891 Å20 Å2
3---1.6038 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.98→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 26 308 8498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088394HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9611483HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2681SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1402HARMONIC5
X-RAY DIFFRACTIONt_it8394HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1151SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6910SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion14.16
LS refinement shellResolution: 1.98→2 Å
RfactorNum. reflection% reflection
Rfree0.3635 86 -
Rwork0.3567 --
obs0.357 1727 79.92 %
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)
10.4839-2.19632.3513.5198-5.802912.1358-0.08870.1374-0.92710.1374-0.30390.3364-0.92710.33640.39260.0599-0.1060.0342-0.04470.0358-0.05642.8495-29.1927-41.1297
20.8477-0.25431.4660.6031-1.34614.63860.0962-0.0068-0.0552-0.0068-0.18360.2375-0.05520.23750.0874-0.00260.03050.0476-0.01020.02-0.06050.5026-36.9599-42.7195
30.7078-0.5039-0.19690.74850.02253.1549-0.0557-0.0676-0.1453-0.06760.0612-0.1358-0.1453-0.1358-0.0055-0.00690.01690.0359-0.04770.0163-0.0382-8.3141-37.2016-39.8393
41.0958-0.17321.56970.4524-1.29114.56720.06560.0502-0.34140.05020.0226-0.1277-0.3414-0.1277-0.08820.01550.04110.0376-0.03420.0176-0.0651-6.5095-32.9505-40.6405
51.0208-0.2735-1.0540-0.65171.94420.16610.3541-1.02930.3541-0.06460.0267-1.02930.0267-0.10150.1013-0.00210.041-0.0992-0.0053-0.0623-3.3695-27.0928-41.1634
64.14131.2221-3.79924.2326-5.40630.39580.15660.0981-0.83040.0981-0.5126-0.4419-0.8304-0.44190.3560.11920.1743-0.0548-0.09870.0068-0.1281-17.1931-24.0776-22.7181
70.46340.47590.07842.8828-0.40131.9011-0.1495-0.1023-0.426-0.1023-0.14-0.0224-0.426-0.02240.28950.07570.0479-0.0406-0.0453-0.0061-0.0958-10.5707-27.5516-20.1195
80.1624-1.23910.2332.5245-2.57615.5482-0.1960.3755-0.40110.3755-0.05150.2464-0.40110.24640.24740.0011-0.0007-0.0319-0.0538-0.01-0.0398-3.8282-34.3046-17.8431
92.86392.3061-1.11532.5006-0.82962.21760.07090.3748-0.83710.3748-0.33850.082-0.83710.0820.26760.1407-0.0526-0.1051-0.10240.006-0.0782-6.9512-24.1929-15.8206
100.2517-1.50010.56261.22711.00761.7157-0.1588-0.1069-0.3298-0.10690.01430.0169-0.32980.01690.14450.05650.01420.0013-0.05730.0207-0.0545-10.8687-29.1435-26.587
110.8861-0.15360.34062.7401-1.50161.269-0.0581-0.2260.2637-0.2260.0979-0.11690.2637-0.1169-0.0398-0.0164-0.0312-0.01630.0174-0.011-0.0607-18.1759-71.5276-33.669
122.14-0.06331.00313.96560.3347.8675-0.0291-0.2250.2773-0.225-0.0423-0.56010.2773-0.56010.0714-0.0757-0.0912-0.0363-0.076-0.01270.0049-24.3556-78.6451-31.8857
131.5513-2.64372.89877.4474-4.28214.0228-0.23670.3564-0.15320.35640.5165-0.2597-0.1532-0.2597-0.2797-0.1349-0.01570.0140.03740.00460.0811-31.4541-69.6995-26.2513
141.5140.8818-0.0681.1068-0.09770-0.0749-0.08930.0027-0.08930.1256-0.11070.0027-0.1107-0.0507-0.0429-0.0196-0.03560.02550.0281-0.0102-19.485-62.27-31.7184
152.15530.9886-0.86921.1242-0.84121.5738-0.0289-0.06330.1281-0.06330.1087-0.04140.1281-0.0414-0.0798-0.0432-0.0119-0.0299-0.0135-0.0115-0.0494-19.1484-63.96-32.9017
161.23791.5773-0.46282.8112-1.69170.3116-0.03990.04650.19820.04650.09280.05640.19820.0564-0.05290.04890.0004-0.0348-0.0158-0.0204-0.0333-7.6263-68.565815.8821
170.30130.42760.11561.7003-0.5560.7812-0.0075-0.06260.1344-0.06260.10660.08680.13440.0868-0.0991-0.02140.0219-0.0228-0.0176-0.0243-0.026-0.8652-54.72467.7737
180.72851.0286-0.58041.6982-1.04421.9036-0.0073-0.09430.0556-0.09430.1462-0.20340.0556-0.2034-0.1389-0.0331-0.0005-0.0569-0.0239-0.0193-0.0287-12.7467-59.60235.9847
190.5825-0.03150.17271.21220.19490.08680.01370.10730.07120.10730.0254-0.01140.0712-0.0114-0.03910.00760.0076-0.02-0.0219-0.0031-0.0475-0.6264-52.24812.792
203.22112.5768-5.820801.62594.0301-0.17490.15220.00060.15220.0129-0.27620.0006-0.27620.16190.06770.013-0.0095-0.08590.0068-0.0572-11.6904-57.336418.5466
210.66440.0851-0.33532.25350.5870.7291-0.04770.17870.11590.17870.02440.04920.11590.04920.0233-0.01950.0281-0.006-0.0176-0.0036-0.03750.6562-66.2109-19.7926
227.9493-1.3510.07181.68622.42061.2681-0.0820.266-0.30330.2660.12830.018-0.30330.018-0.0463-0.05160.0776-0.0085-0.04280.0159-0.00449.4675-70.2614-17.6764
230.90280.1659-0.126811.28134.63911.9509-0.047-0.356-0.0868-0.3560.10490.2108-0.08680.2108-0.0579-0.08670.02060.02150.02040.0202-0.011511.4786-59.9611-26.3081
241.24620.0375-0.25751.0629-0.26010.59180.0195-0.01340.0561-0.01340.005-0.01210.0561-0.0121-0.0245-0.0265-0.0009-0.0016-0.02820.0007-0.0301-2.256-58.6011-22.8693
250.268-0.1295-0.40971.42620.68742.2060.01630.12170.09740.1217-0.0166-0.04560.0974-0.04560.0003-0.0197-0.0004-0.003-0.01930.0029-0.0398-5.1856-58.6094-20.3353
260-1.3334-0.024.14691.39380.41570.13630.35080.08780.3508-0.087-0.10560.0878-0.1056-0.04930.0972-0.0089-0.0444-0.01650.004-0.0533-0.7517-68.1932.9299
270.6838-0.37540.25651.2955-0.13991.48540.00570.3056-0.07340.3056-0.0562-0.0345-0.0734-0.03450.05060.0752-0.0203-0.0229-0.0282-0.0236-0.1559-0.9113-52.715437.5208
2800.61770.66473.48320.64222.75010.02450.52860.12110.5286-0.08870.26050.12110.26050.06420.0899-0.0529-0.1249-0.05240.0418-0.11379.4194-62.603940.1305
290.8255-0.4590.22910.3999-1.1061.60660.0280.2568-0.1690.2568-0.04660.0042-0.1690.00420.01860.1037-0.0309-0.0379-0.0761-0.0214-0.08771.2008-52.596632.3605
300.5986-0.24770.54160.5714-0.45230.5982-0.01160.2293-0.15640.2293-0.0187-0.018-0.1564-0.0180.03030.0851-0.0063-0.0322-0.0287-0.0178-0.08242.9234-50.904432.2124
319.51422.18451.13877.60910.67095.4591-0.2088-0.0945-0.8123-0.09450.29140.5267-0.81230.5267-0.0825-0.0723-0.1170.03970.0214-0.08980.022812.8598-18.645811.9925
322.4948-0.72950.23462.3396-0.29391.61790.1256-0.1996-0.1653-0.19960.04490.0332-0.16530.0332-0.1705-0.038-0.00620.0479-0.0111-0.00770.01159.1696-23.5386.8608
333.8779-2.8937-0.34484.49621.32520.83720.1819-0.5156-0.0596-0.51560.0086-0.035-0.0596-0.035-0.1906-0.0594-0.01180.02770.0172-0.0019-0.03635.4501-31.37454.7098
341.078-0.3679-0.54130.7894-0.31671.41680.12250.0028-0.04660.0028-0.0125-0.1218-0.0466-0.1218-0.1101-0.0681-0.00280.02690.00030.0083-0.00427.2123-25.50464.3101
350.4177-1.3915-2.386701.92947.13940.1881-0.0062-0.4559-0.0062-0.00610.1746-0.45590.1746-0.1819-0.0802-0.01170.0445-0.09670.02030.08556.7511-14.70878.986
361.4943-1.0979-1.05272.53462.55232.328-0.0957-0.0742-0.0149-0.0742-0.0282-0.1337-0.0149-0.13370.1239-0.10270.02450.00080.00430.00410.0132-14.6914-23.809915.5843
378.5579-1.6346-4.1070-1.65011.21770.21580.4474-0.05520.44740.06290.0606-0.05520.0606-0.2786-0.06570.025-0.0050.0187-0.08550.0262-1.1415-17.621619.2061
381.5823-0.4094-0.05091.0870.86023.4532-0.20510.22860.27560.22860.1840.12020.27560.12020.0211-0.05150.07140.0350.02120.0293-0.0348-7.6121-29.516224.3379
391.4124-1.041-0.63741.4871.4661.3563-0.0819-0.02650.0334-0.02650.08390.01790.03340.0179-0.002-0.08730.00690.0009-0.00670.00740.0077-9.2159-23.663617.6645
401.18713.19753.55772.04563.42850.95290.0216-0.3648-0.3052-0.3648-0.11360.2582-0.30520.25820.0921-0.03590.0042-0.0169-0.0174-0.03880.0611-12.5232-12.21919.4933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 13}A1 - 13
2X-RAY DIFFRACTION2{A|14 - 33}A14 - 33
3X-RAY DIFFRACTION3{A|34 - 73}A34 - 73
4X-RAY DIFFRACTION4{A|74 - 95}A74 - 95
5X-RAY DIFFRACTION5{A|96 - 108}A96 - 107
6X-RAY DIFFRACTION6{B|1 - 12}B1 - 12
7X-RAY DIFFRACTION7{B|13 - 44}B13 - 44
8X-RAY DIFFRACTION8{B|45 - 66}B45 - 66
9X-RAY DIFFRACTION9{B|67 - 96}B67 - 96
10X-RAY DIFFRACTION10{B|97 - 121}B97 - 120
11X-RAY DIFFRACTION11{C|467 - 520}C467 - 520
12X-RAY DIFFRACTION12{C|521 - 536}C521 - 536
13X-RAY DIFFRACTION13{C|537 - 544}C537 - 544
14X-RAY DIFFRACTION14{C|545 - 589}C545 - 589
15X-RAY DIFFRACTION15{C|590 - 622}C590 - 622
16X-RAY DIFFRACTION16{D|467 - 491}D467 - 491
17X-RAY DIFFRACTION17{D|492 - 520}D492 - 520
18X-RAY DIFFRACTION18{D|521 - 549}D521 - 549
19X-RAY DIFFRACTION19{D|550 - 609}D550 - 609
20X-RAY DIFFRACTION20{D|610 - 618}D610 - 618
21X-RAY DIFFRACTION21{E|467 - 520}E467 - 520
22X-RAY DIFFRACTION22{E|521 - 532}E521 - 532
23X-RAY DIFFRACTION23{E|533 - 548}E533 - 548
24X-RAY DIFFRACTION24{E|549 - 594}E549 - 594
25X-RAY DIFFRACTION25{E|595 - 618}E595 - 617
26X-RAY DIFFRACTION26{F|467 - 491}F467 - 491
27X-RAY DIFFRACTION27{F|492 - 524}F492 - 524
28X-RAY DIFFRACTION28{F|525 - 544}F525 - 544
29X-RAY DIFFRACTION29{F|545 - 567}F545 - 567
30X-RAY DIFFRACTION30{F|568 - 622}F568 - 622
31X-RAY DIFFRACTION31{G|1 - 12}G1 - 12
32X-RAY DIFFRACTION32{G|13 - 44}G13 - 44
33X-RAY DIFFRACTION33{G|45 - 59}G45 - 59
34X-RAY DIFFRACTION34{G|60 - 110}G60 - 110
35X-RAY DIFFRACTION35{G|111 - 121}G111 - 119
36X-RAY DIFFRACTION36{H|1 - 35}H1 - 35
37X-RAY DIFFRACTION37{H|36 - 45}H36 - 45
38X-RAY DIFFRACTION38{H|46 - 68}H46 - 68
39X-RAY DIFFRACTION39{H|69 - 98}H69 - 98
40X-RAY DIFFRACTION40{H|99 - 108}H99 - 107

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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