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- PDB-6vjt: Co-crystals of broadly neutralizing antibody with the linear epit... -

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Basic information

Entry
Database: PDB / ID: 6vjt
TitleCo-crystals of broadly neutralizing antibody with the linear epitope from Hepatitis B surface antigen
Components
  • Heavy Chain Fab Fragment of Monoclonal Ab15
  • Light Chain Fab Fragment of Monoclonal antibody A15
  • antigenic region 139-148 of Hepatitis B surface antigen protein
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / Hepatitis B / HepB / Fab / Ab / antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / caveolin-mediated endocytosis of virus by host cell / membrane => GO:0016020 / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / Large envelope protein
Function and homology information
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsOren, D.A. / Nussenzweig, M.C. / Wang, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PHS AI129795 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations.
Authors: Wang, Q. / Michailidis, E. / Yu, Y. / Wang, Z. / Hurley, A.M. / Oren, D.A. / Mayer, C.T. / Gazumyan, A. / Liu, Z. / Zhou, Y. / Schoofs, T. / Yao, K.H. / Nieke, J.P. / Wu, J. / Jiang, Q. / ...Authors: Wang, Q. / Michailidis, E. / Yu, Y. / Wang, Z. / Hurley, A.M. / Oren, D.A. / Mayer, C.T. / Gazumyan, A. / Liu, Z. / Zhou, Y. / Schoofs, T. / Yao, K.H. / Nieke, J.P. / Wu, J. / Jiang, Q. / Zou, C. / Kabbani, M. / Quirk, C. / Oliveira, T. / Chhosphel, K. / Zhang, Q. / Schneider, W.M. / Jahan, C. / Ying, T. / Horowitz, J. / Caskey, M. / Jankovic, M. / Robbiani, D.F. / Wen, Y. / de Jong, Y.P. / Rice, C.M. / Nussenzweig, M.C.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy Chain Fab Fragment of Monoclonal Ab15
L: Light Chain Fab Fragment of Monoclonal antibody A15
P: antigenic region 139-148 of Hepatitis B surface antigen protein


Theoretical massNumber of molelcules
Total (without water)48,4173
Polymers48,4173
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-33 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.848, 71.150, 134.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy Chain Fab Fragment of Monoclonal Ab15


Mass: 24024.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: IGgamma1 / Details (production host): von Boehmer et al., 2016 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light Chain Fab Fragment of Monoclonal antibody A15


Mass: 23310.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: IGchai / Details (production host): von Boehmer et al., 2016 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide antigenic region 139-148 of Hepatitis B surface antigen protein


Mass: 1081.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus / References: UniProt: A0A5A4RHH5*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.36 % / Description: plates
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: Morpheus position E1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2019
Details: Cryogenically-cooled single crystal Si(220) side bounce monochromator.
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→134.7 Å / Num. obs: 46432 / % possible obs: 99.5 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 17.2 / Num. measured all: 598818
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.8212.11.2562847623560.7930.3661.311.391
9.09-134.710.70.04546974380.9990.0140.04847.399.9

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDS1.11.7data reduction
XDS0.5.32data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGU

5ggu


Resolution: 1.782→67.352 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1999 4.31 %random
Rwork0.1816 44329 --
obs0.1835 46328 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 39.4993 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 1.782→67.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 361 3738
Biso mean---43.72 -
Num. residues----447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.782-1.82650.29251290.2762287092
1.8265-1.87590.28141410.23723130100
1.8759-1.93110.27491420.21943149100
1.9311-1.99340.26221420.21163142100
1.9934-2.06470.28961410.20723126100
2.0647-2.14730.23591420.19253148100
2.1473-2.24510.22571430.18653172100
2.2451-2.36340.24211440.20033179100
2.3634-2.51150.24761420.19433155100
2.5115-2.70540.27031430.20933181100
2.7054-2.97770.26461450.20563200100
2.9777-3.40860.21591440.18633211100
3.4086-4.29430.22041470.16143252100
4.2943-67.3520.17611540.15133414100

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