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- PDB-9iy2: Immune complex of HEV-E2s, nAb 8C11 and nAb 8H3 -

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Basic information

Entry
Database: PDB / ID: 9iy2
TitleImmune complex of HEV-E2s, nAb 8C11 and nAb 8H3
Components
  • Heavy Chain of mAb 8C11
  • Heavy Chain of mAb 8H3
  • Light Chain of mAb 8C11
  • Light Chain of mAb 8H3
  • Secreted protein ORF2
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell Golgi apparatus / host cell surface / 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
Mus sp. (mice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.476 Å
AuthorsMinghua, Z. / Lizhi, Z. / Ying, G. / Shaowei, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structural basis for the synergetic neutralization of hepatitis E virus by antibody-antibody interaction
Authors: Minghua, Z. / Lizhi, Z. / Ying, G. / Shaowei, L. / Ningshao, X.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_id_CSD
Revision 1.2Oct 30, 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: Secreted protein ORF2
H: Heavy Chain of mAb 8C11
L: Light Chain of mAb 8C11
B: Secreted protein ORF2
C: Light Chain of mAb 8C11
D: Heavy Chain of mAb 8C11
E: Heavy Chain of mAb 8H3
F: Light Chain of mAb 8H3
G: Heavy Chain of mAb 8H3
I: Light Chain of mAb 8H3


Theoretical massNumber of molelcules
Total (without water)238,15910
Polymers238,15910
Non-polymers00
Water00
1
A: Secreted protein ORF2
H: Heavy Chain of mAb 8C11
L: Light Chain of mAb 8C11
G: Heavy Chain of mAb 8H3
I: Light Chain of mAb 8H3


Theoretical massNumber of molelcules
Total (without water)119,0805
Polymers119,0805
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted protein ORF2
C: Light Chain of mAb 8C11
D: Heavy Chain of mAb 8C11
E: Heavy Chain of mAb 8H3
F: Light Chain of mAb 8H3


Theoretical massNumber of molelcules
Total (without water)119,0805
Polymers119,0805
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.465, 248.941, 76.841
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Secreted protein ORF2 / E2s / ORF2s


Mass: 23117.691 Da / Num. of mol.: 2
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 Heavy Chain of mAb 8C11


Mass: 24476.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice) / Plasmid details: Ascites
#3: Antibody Light Chain of mAb 8C11


Mass: 23648.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice) / Plasmid details: Ascites
#4: Antibody Heavy Chain of mAb 8H3


Mass: 23599.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)
#5: Antibody Light Chain of mAb 8H3


Mass: 24237.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)
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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 0.2M MgSO4 + 8% glycerinum + 11% PEG 40,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.476→50 Å / Num. obs: 32075 / % possible obs: 93.48 % / Redundancy: 3.5 % / Rpim(I) all: 0.124 / Rrim(I) all: 0.237 / Net I/σ(I): 6.81
Reflection shellResolution: 3.476→3.601 Å / Num. unique obs: 2967 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RKD,4M61,2DTG

3rkd

4m61

2dtg
PDB Unreleased entry


Resolution: 3.476→36.651 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1542 4.81 %
Rwork0.2234 --
obs0.2256 32052 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.476→36.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15430 0 0 0 15430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915824
X-RAY DIFFRACTIONf_angle_d1.63321572
X-RAY DIFFRACTIONf_dihedral_angle_d13.9235596
X-RAY DIFFRACTIONf_chiral_restr0.0722471
X-RAY DIFFRACTIONf_plane_restr0.0082725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4764-3.58860.35351250.29892563X-RAY DIFFRACTION86
3.5886-3.71670.35671370.29192670X-RAY DIFFRACTION91
3.7167-3.86540.32441370.28812691X-RAY DIFFRACTION91
3.8654-4.04110.29271290.26282691X-RAY DIFFRACTION90
4.0411-4.25380.28221480.24192693X-RAY DIFFRACTION91
4.2538-4.51990.25031070.21412769X-RAY DIFFRACTION92
4.5199-4.86810.23941410.2022744X-RAY DIFFRACTION93
4.8681-5.35670.24691430.22815X-RAY DIFFRACTION95
5.3567-6.12870.24821630.21312910X-RAY DIFFRACTION98
6.1287-7.70970.29041730.22532966X-RAY DIFFRACTION100
7.7097-36.6510.21271390.17062998X-RAY DIFFRACTION100
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)
13.2187-0.9619-1.31662.7175-0.11482.1336-0.0424-0.09850.16080.0207-0.02610.50090.0611-0.09020.08110.54670.0101-0.08110.4523-0.06780.681462.249121.063414.5815
22.11770.28290.0943.26820.10231.2762-0.0165-0.0705-0.20570.4628-0.00430.0770.4676-0.0720.07440.62070.01530.06240.50590.00460.377336.9867-15.126114.0837
31.82470.69480.13642.76010.03113.02660.2928-0.4577-0.5970.6997-0.2066-0.16370.97040.4011-0.07710.92470.145-0.09990.74160.14430.698445.5307-20.936528.5095
42.40310.8682-0.05172.30542.33722.91880.1784-0.09240.02620.03040.0832-0.16280.35610.1602-0.22910.51560.0387-0.10510.34250.04820.556186.718523.229614.248
56.26211.68890.4564.9823-0.62662.36940.1217-0.3870.23410.3049-0.1951-0.3787-0.1121-0.05570.28780.6580.05620.09330.5227-0.03070.39101.705849.782527.3829
61.1896-0.0008-0.09084.5442-1.33671.04740.17720.11260.1778-0.1033-0.0827-0.0444-0.18920.1248-0.12370.61080.03110.05890.6345-0.07560.5518111.701859.0547.8451
72.53021.51130.79992.19411.11312.7823-0.27010.78290.1689-0.50490.29140.2913-0.17030.17760.05130.61710.0271-0.09390.67380.10820.589686.4794-6.2517-13.2422
83.33271.2442-0.17811.45321.14224.1916-0.32150.9615-0.4088-0.47170.07750.32490.173-0.00470.26840.74570.0289-0.14230.697-0.08040.746173.1782-17.7689-11.9595
94.8744-0.7640.19771.4017-1.15241.39850.51861.7125-0.4197-0.3734-0.4732-0.02570.40030.18440.08360.75010.3094-0.10151.0464-0.19420.674262.231945.4658-17.537
105.5714-0.67640.09842.4286-0.42883.7250.49052.06880.571-0.5443-0.4559-0.4816-0.2915-0.00050.15320.68640.26070.25611.25230.2110.607775.865156.81-18.4122
111.2208-0.3618-0.22483.5222-1.89265.09890.0784-0.08120.23220.19790.38650.3917-0.8109-1.0107-0.50371.04420.04980.2390.652-0.01591.1455103.669983.855915.1028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 459 through 604)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 224)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 213)
4X-RAY DIFFRACTION4(chain 'B' and resid 460 through 604)
5X-RAY DIFFRACTION5(chain 'C' and resid 1 through 106)
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 224)
7X-RAY DIFFRACTION7(chain 'E' and resid 1 through 219)
8X-RAY DIFFRACTION8(chain 'F' and resid 1 through 217)
9X-RAY DIFFRACTION9(chain 'G' and resid 1 through 219)
10X-RAY DIFFRACTION10(chain 'I' and resid 1 through 217)
11X-RAY DIFFRACTION11(chain 'C' and resid 109 through 213)

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