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- PDB-8ef3: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ119-D -

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Basic information

Entry
Database: PDB / ID: 8ef3
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ119-D
Components
  • rhMZ119-D antibody heavy chain
  • rhMZ119-D antibody light chain
KeywordsVIRAL PROTEIN / ZIKV / ZIKV-specific / cross-protomer epitopes
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.672 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
A: rhMZ119-D antibody heavy chain
B: rhMZ119-D antibody light chain
C: rhMZ119-D antibody heavy chain
D: rhMZ119-D antibody light chain


Theoretical massNumber of molelcules
Total (without water)92,2244
Polymers92,2244
Non-polymers00
Water18,2311012
1
A: rhMZ119-D antibody heavy chain
B: rhMZ119-D antibody light chain


Theoretical massNumber of molelcules
Total (without water)46,1122
Polymers46,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area19970 Å2
MethodPISA
2
C: rhMZ119-D antibody heavy chain
D: rhMZ119-D antibody light chain


Theoretical massNumber of molelcules
Total (without water)46,1122
Polymers46,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.243, 71.015, 103.741
Angle α, β, γ (deg.)90.000, 102.380, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12(chain B and (resid 1 through 52 or resid 54 through 211))
22(chain D and (resid 1 through 52 or resid 54 through 211))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLUGLUchain AAA1 - 2181 - 218
211GLUGLUGLUGLUchain CCC1 - 2181 - 218
112SERSERLYSLYS(chain B and (resid 1 through 52 or resid 54 through 211))BB1 - 521 - 52
122PROPROALAALA(chain B and (resid 1 through 52 or resid 54 through 211))BB54 - 21154 - 211
212SERSERLYSLYS(chain D and (resid 1 through 52 or resid 54 through 211))DD1 - 521 - 52
222PROPROALAALA(chain D and (resid 1 through 52 or resid 54 through 211))DD54 - 21154 - 211

NCS ensembles :
ID
1
2

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Components

#1: Antibody rhMZ119-D antibody heavy chain


Mass: 23538.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody rhMZ119-D antibody light chain


Mass: 22573.865 Da / Num. of mol.: 2
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.: 1012 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 8K, 0.2M CaAc hydrate, 0.1M Na Cacodylate (pH6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 114507 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.85 / Rsym value: 0.062 / Net I/σ(I): 21.2
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 11124 / CC1/2: 0.35 / Rsym value: 1.118

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZ2, 5QF1

5tz2

5qf1


Resolution: 1.672→34.305 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 1999 1.89 %
Rwork0.1819 104011 -
obs0.1822 106010 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.01 Å2 / Biso mean: 22.9508 Å2 / Biso min: 5.06 Å2
Refinement stepCycle: final / Resolution: 1.672→34.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6362 0 0 1012 7374
Biso mean---35.94 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036540
X-RAY DIFFRACTIONf_angle_d0.7348926
X-RAY DIFFRACTIONf_chiral_restr0.051008
X-RAY DIFFRACTIONf_plane_restr0.0051134
X-RAY DIFFRACTIONf_dihedral_angle_d11.43914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1933X-RAY DIFFRACTION5.354TORSIONAL
12C1933X-RAY DIFFRACTION5.354TORSIONAL
21B1900X-RAY DIFFRACTION5.354TORSIONAL
22D1900X-RAY DIFFRACTION5.354TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.672-1.71340.2965450.2874236429
1.7134-1.75970.27631030.259534967
1.7597-1.81150.28251490.2505771296
1.8115-1.86990.25921510.2275789899
1.8699-1.93680.2371530.1945797299
1.9368-2.01430.20871550.1798801199
2.0143-2.1060.2061540.17428015100
2.106-2.2170.19031540.16898059100
2.217-2.35580.18491550.17318020100
2.3558-2.53770.21871560.18498072100
2.5377-2.7930.20211550.1858079100
2.793-3.19680.1741560.1748106100
3.1968-4.02670.17631560.16368136100
4.0267-34.3050.17521570.1734821899
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)
10.86560.04070.11991.43740.031.2391-0.0371-0.05550.05130.00370.03490.11710.0373-0.27050.00780.108-0.00430.0010.1547-0.01320.066639.839528.4525-13.3672
21.1176-0.1626-0.39391.4122-0.16581.34040.00510.0934-0.2038-0.0480.02020.13940.04940.0166-0.01770.07460.0250.00270.0491-0.00310.107143.458220.3344-48.8347
31.29070.1016-0.28292.5350.43161.5065-0.01080.195-0.2004-0.2028-0.0290.17060.0392-0.2040.10960.13890.039-0.01810.089-0.03120.133539.140624.842-56.3686
40.7712-0.8549-0.3881.1281-0.09091.7001-0.18940.131-0.1442-0.18830.1589-0.23760.398-0.06320.03690.2392-0.07580.08540.1639-0.0040.145741.30941.3833-16.8012
51.70260.02990.56441.3663-0.14271.4875-0.2847-0.0299-0.087-0.04150.14950.19430.0643-0.3281-0.06650.1518-0.05930.04060.2010.01590.118134.53957.3851-11.6682
60.14170.05270.15260.02310.04270.2154-0.0501-0.0295-0.08310.0575-0.15180.08340.2501-0.311-0.23160.1742-0.09860.04740.1663-0.03060.130739.09333.4752-27.2873
70.58250.11920.06860.81120.18930.86760.0610.03640.217-0.0368-0.0387-0.0156-0.06430.0357-0.00260.0472-0.00390.01670.05680.03430.121152.982311.2096-46.9693
80.4081-0.14610.3270.80640.30030.5140.04510.0540.0859-0.0127-0.0136-0.00440.0233-0.08810.0680.0307-0.00160.02550.0660.03780.110251.76528.2322-46.2264
90.8781-0.0445-0.10881.30490.01831.0684-0.0519-0.0143-0.11890.19120.06370.0170.01330.1098-0.01280.0930.0449-0.00520.1371-0.00040.12399.5564-5.7535-37.1166
101.92210.20640.27531.6878-0.47591.5958-0.0165-0.05150.24990.02560.0230.22430.0976-0.0499-0.02820.19250.005-0.04230.0895-00.1831-3.8659-1.0905-1.7228
110.7647-0.3090.0861.52530.03141.4613-0.1833-0.0630.1380.20850.0535-0.0998-0.14690.0675-0.03120.0814-0.0336-0.04830.13760.00180.14827.880917.7868-38.368
120.33120.1211-0.0690.1604-0.45531.5714-0.05310.0497-0.07410.0888-0.0365-0.0278-0.2374-0.10940.04710.13080.0197-0.02480.1223-0.00490.12295.983911.97-20.9349
130.9368-0.56820.01071.3538-0.45671.18130.03480.0370.1594-0.1891-0.0908-0.1097-0.1597-0.00660.07020.17580.0039-0.0430.07350.0270.1238.077511.7754-2.2671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )A1 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 191 )A119 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 218 )A192 - 218
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 23 )B1 - 23
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 96 )B24 - 96
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 115 )B97 - 115
7X-RAY DIFFRACTION7chain 'B' and (resid 116 through 163 )B116 - 163
8X-RAY DIFFRACTION8chain 'B' and (resid 164 through 211 )B164 - 211
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 118 )C1 - 118
10X-RAY DIFFRACTION10chain 'C' and (resid 119 through 218 )C119 - 218
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 74 )D1 - 74
12X-RAY DIFFRACTION12chain 'D' and (resid 75 through 130 )D75 - 130
13X-RAY DIFFRACTION13chain 'D' and (resid 131 through 211 )D131 - 211

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