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- PDB-9iy0: anti-HEV mAb 8H3 -

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Basic information

Entry
Database: PDB / ID: 9iy0
Titleanti-HEV mAb 8H3
Components
  • Heavy chain of 8H3 Fab
  • Light chain of 8H3 Fab
KeywordsIMMUNE SYSTEM / monoclonal antibody
Biological speciesMus sp. (mice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMinghua, Z. / Lizhi, Z. / Yang, H. / 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.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of 8H3 Fab
H: Heavy chain of 8H3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9356
Polymers47,8372
Non-polymers974
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-49 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.089, 103.062, 52.044
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of 8H3 Fab


Mass: 24237.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice) / Plasmid details: Ascites
#2: Antibody Heavy chain of 8H3 Fab


Mass: 23599.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice) / Plasmid details: Ascites
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 2M Mg(Ac)2 and 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 27054 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rsym value: 0.047 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.97-23.60.54213040.7920.940.3250.6330.81694.6
2-2.043.60.49213180.8490.9580.2940.5740.85795.8
2.04-2.083.60.4413240.8660.9630.270.5181.10996.9
2.08-2.123.70.34713170.9140.9770.2060.4040.91598
2.12-2.173.80.29113800.9440.9860.1730.3390.90498.5
2.17-2.223.80.25613250.9480.9870.1520.2980.92498.4
2.22-2.273.80.24813590.9590.9890.1470.2891.12298.4
2.27-2.343.80.19313250.9740.9930.1140.2240.93398.6
2.34-2.43.80.16813500.9760.9940.10.1960.91799
2.4-2.483.80.13413820.9850.9960.080.1560.90599.1
2.48-2.573.80.11113440.990.9980.0660.130.94198.9
2.57-2.673.80.09613580.990.9970.0570.1121.05599.3
2.67-2.83.80.07113580.9940.9990.0420.0830.94499
2.8-2.943.80.05613530.9960.9990.0330.0660.96899.2
2.94-3.133.80.04513720.9980.9990.0270.0521.05899.2
3.13-3.373.80.04213780.9970.9990.0250.0491.16599.6
3.37-3.713.80.04213720.9970.9990.0250.0481.03399.6
3.71-4.243.70.02913680.99810.0180.0340.93899.8
4.24-5.353.70.02213700.99910.0130.0261.01398.9
5.35-503.80.02813970.9980.9990.0170.0331.17899.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNS

1fns


Resolution: 1.97→25.97 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1433 5.32 %
Rwork0.1917 --
obs0.1939 26956 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 4 232 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043410
X-RAY DIFFRACTIONf_angle_d0.6494649
X-RAY DIFFRACTIONf_dihedral_angle_d5.395465
X-RAY DIFFRACTIONf_chiral_restr0.045527
X-RAY DIFFRACTIONf_plane_restr0.007591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.33291210.26732413X-RAY DIFFRACTION92
2.04-2.130.26981340.2622510X-RAY DIFFRACTION97
2.13-2.220.31431420.24752546X-RAY DIFFRACTION98
2.22-2.340.32011440.24382538X-RAY DIFFRACTION98
2.34-2.490.28451570.24122575X-RAY DIFFRACTION99
2.49-2.680.2871700.2332536X-RAY DIFFRACTION99
2.68-2.950.26961430.22012562X-RAY DIFFRACTION99
2.95-3.370.23321330.19752624X-RAY DIFFRACTION99
3.37-4.250.19671440.16812596X-RAY DIFFRACTION100
4.25-25.970.17881450.14822623X-RAY DIFFRACTION99
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)
10.7404-0.57850.73081.8562-0.35561.00190.0159-0.08810.16270.12690.04410.054-0.0466-0.1784-0.00010.32020.11620.05310.33690.02410.316324.591154.77915.9519
21.2785-1.4243-0.4031.63880.1891.9766-0.1007-0.4008-0.0825-0.01060.259-0.0501-0.27060.38730.00040.3083-0.04390.01010.3445-0.05370.326344.353731.755617.8522
32.0384-0.32980.91560.151-0.31310.70770.149-0.0277-0.4172-0.4323-0.11410.70250.1465-0.9377-0.73060.48680.1498-0.10880.6602-0.0720.331713.58238.948-10.1344
41.3672-0.78070.05950.7912-0.1661.39120.1040.0315-0.1157-0.1796-0.08270.04090.0291-0.4933-0.01940.29560.0172-0.03220.332-0.02590.325627.283533.0528-0.2572
50.5842-0.4897-0.21341.50730.82141.237-0.3022-0.2053-0.08570.3040.22890.31770.3201-0.40190.0020.39080.01490.04320.40470.03870.42834.758518.373922.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 123 )
2X-RAY DIFFRACTION2chain 'H' and (resid 124 through 219 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 38 )
4X-RAY DIFFRACTION4chain 'L' and (resid 39 through 149 )
5X-RAY DIFFRACTION5chain 'L' and (resid 150 through 217 )

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