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

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Basic information

Entry
Database: PDB / ID: 6mty
TitleCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ4 isolated following ZPIV vaccination
Components
  • MZ4 Heavy Chain
  • MZ4 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: 2.951 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
Department of Defense (DOD, United States)W81XWH-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
DepositionOct 22, 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 1.2Oct 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
Revision 1.3Oct 16, 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
H: MZ4 Heavy Chain
L: MZ4 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,0632
Polymers47,0632
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Migrates as heterodimer in Superdex200 Gel-filtration. Also confirmed by SDS PAGE with and without reducing agent. In the absence of reducing agent Heterodimer runs as high ...Evidence: gel filtration, Migrates as heterodimer in Superdex200 Gel-filtration. Also confirmed by SDS PAGE with and without reducing agent. In the absence of reducing agent Heterodimer runs as high molecular weight assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-20 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.358, 67.582, 138.009
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 MZ4 Heavy Chain


Mass: 24031.779 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): Expi 293 / Production host: Homo sapiens (human)
#2: Antibody MZ4 Light Chain


Mass: 23031.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV1-44*01 / Details (production host): pVRC8400 / Cell line (production host): Expi 293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.99 Å3/Da / Density % sol: 58.88 % / Description: Plate like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M HEPES (pH 7.5), 25% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 11975 / % possible obs: 94.4 % / Redundancy: 5 % / Rpim(I) all: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 2.95→3.12 Å / Num. unique obs: 1055 / Rpim(I) all: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTA

4uta


Resolution: 2.951→14.977 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 515 5.01 %
Rwork0.2167 9771 -
obs0.2185 10286 83.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 50.5889 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 2.951→14.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 0 37 3278
Biso mean---38.52 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033328
X-RAY DIFFRACTIONf_angle_d0.7044549
X-RAY DIFFRACTIONf_chiral_restr0.047516
X-RAY DIFFRACTIONf_plane_restr0.005579
X-RAY DIFFRACTIONf_dihedral_angle_d11.6681990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.951-3.24510.338981153254
3.2451-3.70840.2898127240184
3.7084-4.64890.25111490.198284797

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