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- PDB-6nis: Crystal structure of a human anti-ZIKV-DENV neutralizing antibody... -

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Basic information

Entry
Database: PDB / ID: 6nis
TitleCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ24 isolated following ZPIV vaccination
Components
  • MZ24 antibody heavy chain
  • MZ24 antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV-DENV / Antibody / human / Vaccination / ANTIVIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsSankhala, R.S. / Dussupt, V. / Donofrio, G. / Choe, M. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentW81XWH-07-2-0067 United States
CitationJournal: Nat Med / Year: 2020
Title: Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.
Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / ...Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / Abbink, P. / Bai, H. / Bryan, A.L. / Bias, C.H. / Berry, I.M. / Botero, N. / Cook, T. / Doria-Rose, N.A. / Escuer, A.G.I. / Frimpong, J.A. / Geretz, A. / Hernandez, M. / Hollidge, B.S. / Jian, N. / Kabra, K. / Leggat, D.J. / Liu, J. / Pinto, A.K. / Rutvisuttinunt, W. / Setliff, I. / Tran, U. / Townsley, S. / Doranz, B.J. / Rolland, M. / McDermott, A.B. / Georgiev, I.S. / Thomas, R. / Robb, M.L. / Eckels, K.H. / Barranco, E. / Koren, M. / Smith, D.R. / Jarman, R.G. / George, S.L. / Stephenson, K.E. / Barouch, D.H. / Modjarrad, K. / Michael, N.L. / Joyce, M.G. / Krebs, S.J.
History
DepositionDec 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 7, 2021Group: Data collection / Category: reflns / Item: _reflns.pdbx_redundancy
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: MZ24 antibody heavy chain
L: MZ24 antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,27312
Polymers46,8052
Non-polymers46810
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel-filtration and native PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-102 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 66.667, 134.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody MZ24 antibody heavy chain


Mass: 23876.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV4-59*08 / Details (production host): pVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody MZ24 antibody light chain


Mass: 22928.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV1-44*01 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.06 Å3/Da / Density % sol: 59.75 % / Description: Rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Citric acid/NaOH (pH 4.0), 1M LiCl and 20% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.11→28.8 Å / Num. obs: 35154 / % possible obs: 99.7 % / Rsym value: 0.1 / Net I/σ(I): 12.8
Reflection shellResolution: 2.11→2.12 Å / Num. unique obs: 5276 / Rsym value: 0.677

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MTX

6mtx


Resolution: 2.113→14.984 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1668 4.99 %
Rwork0.1647 --
obs0.1665 33454 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.113→14.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 20 357 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033375
X-RAY DIFFRACTIONf_angle_d0.7674613
X-RAY DIFFRACTIONf_dihedral_angle_d14.3932021
X-RAY DIFFRACTIONf_chiral_restr0.048529
X-RAY DIFFRACTIONf_plane_restr0.005587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.113-2.1750.25621330.22122553X-RAY DIFFRACTION98
2.175-2.2450.24611360.20932615X-RAY DIFFRACTION100
2.245-2.3250.29951400.20322607X-RAY DIFFRACTION100
2.325-2.41770.23851340.20842604X-RAY DIFFRACTION100
2.4177-2.52720.26151410.20352639X-RAY DIFFRACTION100
2.5272-2.65980.22971390.19642643X-RAY DIFFRACTION100
2.6598-2.82540.2451370.18362627X-RAY DIFFRACTION100
2.8254-3.04190.19661390.17772662X-RAY DIFFRACTION100
3.0419-3.34490.19981360.16492652X-RAY DIFFRACTION100
3.3449-3.82190.18651440.14712659X-RAY DIFFRACTION100
3.8219-4.78890.16461440.12882712X-RAY DIFFRACTION100
4.7889-14.98430.16911450.1512813X-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)
16.32620.7172-0.20283.2603-0.64494.7845-0.19450.19250.6199-0.34640.17820.444-0.1565-0.48990.02160.24250.0198-0.05090.25050.02350.364341.658524.816359.1475
20.4756-0.3527-0.23210.69290.41241.18610.0345-0.0027-0.0811-0.0921-0.0460.1165-0.0047-0.17310.01070.2708-0.0194-0.02290.2586-0.00090.312953.593115.630141.7808
32.3856-0.2123-1.67772.2182-0.41913.4384-0.32160.1157-0.2734-0.29980.1113-0.20470.57050.02840.16550.3223-0.01970.0930.2882-0.02410.299242.28412.627965.7689
42.5378-1.9464-4.21631.62133.01888.3453-0.1948-0.03730.0340.29770.05660.08250.5317-0.22450.1950.22-0.07150.02290.2753-0.03530.338252.6933.136758.3239
52.42510.4347-0.59337.4594-1.21843.88420.0563-0.09660.05910.308-0.0477-0.4879-0.04940.247-0.02260.22560.0002-0.02310.194-0.03930.261871.65274.704136.0753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'H' and (resid 77 through 216 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 93 )
4X-RAY DIFFRACTION4chain 'L' and (resid 94 through 118 )
5X-RAY DIFFRACTION5chain 'L' and (resid 119 through 212 )

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