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- PDB-8ef1: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ103-A -

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Basic information

Entry
Database: PDB / ID: 8ef1
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ103-A
Components
  • rhMZ103-A antibody heavy chain
  • rhMZ103-A antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV / ZIKV-specific / cross-protomer epitopes / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSankhala, R.S. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-07-2-0067 United States
CitationJournal: Cell Rep / Year: 2023
Title: Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes.
Authors: Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Gromowski, G.D. / De La Barrera, R.A. / Larocca, R.A. / Mendez-Rivera, L. / Lee, A. / Choe, M. / Zaky, W. / Mantus, G. / Jensen, J.L. / Chen, W. ...Authors: Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Gromowski, G.D. / De La Barrera, R.A. / Larocca, R.A. / Mendez-Rivera, L. / Lee, A. / Choe, M. / Zaky, W. / Mantus, G. / Jensen, J.L. / Chen, W.H. / Gohain, N. / Bai, H. / McCracken, M.K. / Mason, R.D. / Leggat, D. / Slike, B.M. / Tran, U. / Jian, N. / Abbink, P. / Peterson, R. / Mendes, E.A. / Freitas de Oliveira Franca, R. / Calvet, G.A. / Bispo de Filippis, A.M. / McDermott, A. / Roederer, M. / Hernandez, M. / Albertus, A. / Davidson, E. / Doranz, B.J. / Rolland, M. / Robb, M.L. / Lynch, R.M. / Barouch, D.H. / Jarman, R.G. / Thomas, S.J. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
History
DepositionSep 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: rhMZ103-A antibody heavy chain
L: rhMZ103-A antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,2022
Polymers47,2022
Non-polymers00
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, reduced and native SDS PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-24 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.480, 80.123, 175.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-488-

HOH

21H-511-

HOH

31H-518-

HOH

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Components

#1: Antibody rhMZ103-A antibody heavy chain


Mass: 24690.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody rhMZ103-A antibody light chain


Mass: 22511.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20.0% PEG 4K, 0.2M NaAc, 0.1M Na Citrate (pH5.6)

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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 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.87→19.7 Å / Num. obs: 37647 / % possible obs: 90.5 % / Redundancy: 2.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→1.97 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 5536 / CC1/2: 0.8 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQQ

4fqq


Resolution: 1.87→14.829 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1877 5 %
Rwork0.1726 35683 -
obs0.1741 37560 89.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 37.6923 Å2 / Biso min: 20.72 Å2
Refinement stepCycle: final / Resolution: 1.87→14.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 0 396 3668
Biso mean---45.7 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043360
X-RAY DIFFRACTIONf_angle_d0.7514595
X-RAY DIFFRACTIONf_chiral_restr0.051517
X-RAY DIFFRACTIONf_plane_restr0.005585
X-RAY DIFFRACTIONf_dihedral_angle_d11.4291990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8702-1.92070.31951380.2781261186
1.9207-1.97710.27421470.2344281493
1.9771-2.04070.26841470.2144279592
2.0407-2.11340.25431430.2072272490
2.1134-2.19780.2371440.1988274891
2.1978-2.29750.24531460.1967277291
2.2975-2.41810.22431460.1899277991
2.4181-2.56890.21521460.1919278090
2.5689-2.76610.21571470.1834277191
2.7661-3.04230.21881420.1741272489
3.0423-3.47750.2031440.1639271988
3.4775-4.36270.15261430.1465272888
4.3627-14.8290.17321440.1471271884
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)
11.4962-0.2468-0.10840.60110.47274.90620.05640.2865-0.0044-0.1802-0.03690.0929-0.1738-0.0815-0.02570.2661-0.0139-0.0330.26940.0210.24153.188742.227160.9941
23.95592.4695-0.39015.4196-0.49781.5526-0.044-0.0060.3752-0.0772-0.03850.0314-0.11520.10830.09530.1943-0.0063-0.0040.26320.02320.22513.907162.0383.2923
34.15562.16791.5885.84510.61865.14950.05260.0594-0.2629-0.1913-0.0062-0.31520.34370.3519-0.05790.2780.080.02410.4696-0.01080.25928.800734.256261.3172
43.90170.18140.27453.0076-0.58863.59460.00610.1845-0.0216-0.2263-0.07950.05160.03370.07560.04020.2490.00080.00380.34110.00690.189118.461937.688455.6142
53.3281.11820.93652.58420.8922.9851-0.09060.43990.1708-0.38580.0478-0.1842-0.09470.42550.05950.3689-0.0030.05890.5057-0.00070.301525.360739.559750.055
66.2831.58261.99422.76731.22024.6879-0.07630.0250.0225-0.1864-0.01960.00750.02150.080.10760.27910.0440.0150.2880.01230.208620.146237.250758.8537
70.4347-0.8599-1.26684.52095.93037.84710.15360.18880.2834-0.04820.3848-0.465-0.16520.8001-0.58680.2696-0.00450.02530.42990.01470.366134.168845.809471.6332
85.8776-2.2422-3.69885.09833.25393.14990.10770.21680.2006-0.0403-0.09410.0713-0.3692-0.35910.00150.270.0564-0.03730.38980.03460.251919.274458.843292.785
95.0159-4.254-5.44764.9735.32816.4374-0.1043-0.2747-0.0770.33270.2083-0.13180.4160.7736-0.11810.2275-0.0267-0.01740.27790.01020.33830.41648.371789.2534
104.6008-1.1163-1.95832.57120.86568.2040.06770.0444-0.093-0.0541-0.0846-0.0157-0.2725-0.39960.07490.1965-0.0209-0.0140.21550.04240.263122.581551.365291.7207
116.9053-1.4911-3.60494.13792.15892.43870.0522-0.7130.51070.22660.3504-0.4662-0.02150.4137-0.3320.29060.0549-0.04640.3886-0.01060.322630.732255.369195.9881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 135 )H1 - 135
2X-RAY DIFFRACTION2chain 'H' and (resid 136 through 229 )H136 - 229
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 23 )L2 - 23
4X-RAY DIFFRACTION4chain 'L' and (resid 24 through 49 )L24 - 49
5X-RAY DIFFRACTION5chain 'L' and (resid 50 through 76 )L50 - 76
6X-RAY DIFFRACTION6chain 'L' and (resid 77 through 104 )L77 - 104
7X-RAY DIFFRACTION7chain 'L' and (resid 105 through 117 )L105 - 117
8X-RAY DIFFRACTION8chain 'L' and (resid 118 through 143 )L118 - 143
9X-RAY DIFFRACTION9chain 'L' and (resid 144 through 154 )L144 - 154
10X-RAY DIFFRACTION10chain 'L' and (resid 155 through 191 )L155 - 191
11X-RAY DIFFRACTION11chain 'L' and (resid 192 through 213 )L192 - 213

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