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- PDB-9imx: Immune complex of HEV E2s and P1-5B nanobody -

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Basic information

Entry
Database: PDB / ID: 9imx
TitleImmune complex of HEV E2s and P1-5B nanobody
Components
  • P1-5B nanobody
  • Secreted protein ORF2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immune complex / hepatitis E virus / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell surface / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding
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
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTingting, L. / Wenhui, X. / Ying, G. / Shaowei, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Immune complex of HEV E2s and P1-5B nanobody
Authors: Tingting, L. / Wenhui, X. / Ying, G. / Shaowei, L.
History
DepositionJul 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted protein ORF2
B: Secreted protein ORF2
C: P1-5B nanobody
D: P1-5B nanobody
E: Secreted protein ORF2
F: Secreted protein ORF2
G: P1-5B nanobody
H: P1-5B nanobody


Theoretical massNumber of molelcules
Total (without water)121,5708
Polymers121,5708
Non-polymers00
Water2,126118
1
A: Secreted protein ORF2
C: P1-5B nanobody


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted protein ORF2
D: P1-5B nanobody


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Secreted protein ORF2
G: P1-5B nanobody


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Secreted protein ORF2
H: P1-5B nanobody


Theoretical massNumber of molelcules
Total (without water)30,3932
Polymers30,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.393, 51.402, 265.172
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number3
Space group name H-MP121
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

#1: Protein
Secreted protein ORF2 / ORF2s


Mass: 15930.776 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus (strain Pakistan) / Gene: ORF2
Production host: Bacterial expression vector pET-11a (others)
References: UniProt: P33426
#2: Antibody
P1-5B nanobody


Mass: 14461.772 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca)
Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 6% isopropanol, 0.1M sodium acetate pH 4.5, 20% PEG MME550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→66.22 Å / Num. obs: 70266 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.929 / Rpim(I) all: 0.12 / Rrim(I) all: 0.314 / Net I/σ(I): 4.9
Reflection shellResolution: 2.2→2.31 Å / Num. unique obs: 66929 / CC1/2: 0.379 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GGQ,7KN5

3ggq

7kn5


Resolution: 2.2→66.22 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.837 / SU B: 6.97 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2000 2.8 %RANDOM
Rwork0.2168 ---
obs0.27511 68192 85.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.063 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å2-4.36 Å2
2--4.46 Å20 Å2
3----9.22 Å2
Refinement stepCycle: 1 / Resolution: 2.2→66.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 0 118 7390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0117438
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166744
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6410152
X-RAY DIFFRACTIONr_angle_other_deg0.5411.5615442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5855942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.769540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.372101038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021824
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1062.5523828
X-RAY DIFFRACTIONr_mcbond_other3.1052.5523828
X-RAY DIFFRACTIONr_mcangle_it4.3084.5794750
X-RAY DIFFRACTIONr_mcangle_other4.3084.5794751
X-RAY DIFFRACTIONr_scbond_it2.4922.4323610
X-RAY DIFFRACTIONr_scbond_other2.4922.4323611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5424.525403
X-RAY DIFFRACTIONr_long_range_B_refined5.18924.538975
X-RAY DIFFRACTIONr_long_range_B_other5.18824.538967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %
Refinement TLS params.

Method: refined / 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)
10.2756-0.14560.17190.3814-0.13980.11550.00320.0098-0.0080.03110.00150.0119-0.01060.0078-0.00480.1368-0.0072-0.0160.0898-0.02310.009-3.408432.51718.2279
20.3840.2901-0.04160.2278-0.03510.00610.0233-0.04570.0094-0.0179-0.0240.00890.01230.00210.00070.15220.0041-0.01360.0819-0.0120.0029-1.702910.550828.0543
30.01050.062-0.00320.4684-0.01690.00190.0207-0.01250.00220.0166-0.02990.0526-0.00150.01130.00920.110.0058-0.01640.11540.01420.054715.047610.44554.9412
40.2288-0.23460.02870.264-0.01830.009-0.01040.0380.02320.01250.0136-0.0322-0.00160.0302-0.00330.1377-0.002-0.00210.14590.0040.032813.183136.090340.8722
50.3417-0.07340.06320.3459-0.2420.16980.01670.00290.02790.0307-0.00210.0205-0.0231-0.0007-0.01470.12280.011-0.00250.11170.00440.055213.866534.970170.6366
60.5416-0.033-0.07720.09810.00420.0129-0.004-0.0164-0.0440.06570.00450.05120.0099-0.0089-0.00050.1496-0.0074-0.02470.10720.00210.0607-8.3731.041478.9489
70.0366-0.1132-0.08550.36960.26120.201-0.016-0.0088-0.00150.0050.01220.01770.05080.01290.00370.1419-0.0003-0.01360.14660.00620.0578-4.4412.56857.5806
80.11540.06750.2190.65840.03250.4923-0.03920.053-0.01590.0160.05190.06150.01060.1189-0.01270.16650.00490.00370.12930.00470.091717.617120.969894.8178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A457 - 602
2X-RAY DIFFRACTION2B459 - 602
3X-RAY DIFFRACTION3C1 - 109
4X-RAY DIFFRACTION4D2 - 109
5X-RAY DIFFRACTION5E457 - 602
6X-RAY DIFFRACTION6F459 - 602
7X-RAY DIFFRACTION7G1 - 109
8X-RAY DIFFRACTION8H2 - 109

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