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- PDB-8ef2: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ107-B -

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Basic information

Entry
Database: PDB / ID: 8ef2
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ107-B
Components
  • rhMZ107-B antibody heavy chain
  • rhMZ107-B antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV / ZIKV-specific / cross-protomer epitopes / VIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: rhMZ107-B antibody heavy chain
L: rhMZ107-B antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8933
Polymers47,7982
Non-polymers951
Water6,774376
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 area3660 Å2
ΔGint-28 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.235, 118.672, 119.515
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 rhMZ107-B antibody heavy chain


Mass: 24365.205 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 rhMZ107-B antibody light chain


Mass: 23432.850 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 23.5% PEG 4K, 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / 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: 2.1→50 Å / Num. obs: 32733 / % possible obs: 93.2 % / Redundancy: 4 % / CC1/2: 0.86 / Rsym value: 0.12 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 2905 / CC1/2: 0.54 / Rsym value: 0.629

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQQ

4fqq


Resolution: 2.102→14.834 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1626 4.99 %
Rwork0.1722 30973 -
obs0.1744 32599 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.79 Å2 / Biso mean: 36.8104 Å2 / Biso min: 14.47 Å2
Refinement stepCycle: final / Resolution: 2.102→14.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 5 376 3722
Biso mean--41.98 43.35 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073432
X-RAY DIFFRACTIONf_angle_d0.8884686
X-RAY DIFFRACTIONf_chiral_restr0.054528
X-RAY DIFFRACTIONf_plane_restr0.006595
X-RAY DIFFRACTIONf_dihedral_angle_d9.9262055
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.102-2.16320.32031180.2542227083
2.1632-2.23280.27581300.2353253194
2.2328-2.31230.25441400.2244262196
2.3123-2.40450.27541420.213265397
2.4045-2.51350.26241410.1996261896
2.5135-2.64530.25491390.1967262596
2.6453-2.810.25541370.1878262896
2.81-3.02530.24131400.1808262195
3.0253-3.32660.24921330.1724261094
3.3266-3.80090.19081370.1595261293
3.8009-4.76220.17621320.1251258492
4.7622-14.8340.14781370.1459260088
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)
11.87720.05910.62533.793-1.15713.0920.2415-0.00930.2277-0.40280.12170.5261-0.621-0.1324-0.03290.42160.00850.04120.0703-0.01740.269329.294384.2169.6667
22.53430.30770.54473.3559-0.48263.50730.1318-0.3199-0.0186-0.1815-0.0150.1526-0.02040.0629-0.18730.1515-0.0109-0.01130.15080.01040.231230.558977.787319.1962
32.0736-0.32811.03323.95590.90352.70520.122-0.56680.16610.1858-0.0216-0.0139-0.25410.3404-0.13210.2165-0.07520.01110.22670.00320.222835.792283.43425.1317
42.19220.7767-0.42233.6326-0.46073.86240.1039-0.15620.3023-0.15510.1790.2877-0.8134-0.0063-0.1130.2977-0.04370.02980.1662-0.01910.249430.467687.253917.6826
51.05850.1213-0.04091.9836-0.52923.19680.0649-0.3364-0.21540.22120.01560.044-0.2006-0.2653-0.03690.1548-0.0452-0.00230.26650.05930.25134.055271.450725.6572
61.6093-0.72030.0761.06780.53990.38590.31210.0568-0.044-0.24670.00730.3448-0.62110.0862-0.07080.3596-0.0060.00250.1443-0.010.181933.15680.30436.2382
71.9098-0.7373-0.57178.34472.90523.15240.04250.3259-0.1862-0.72610.0616-0.6402-0.5744-0.177-0.07620.3243-0.0244-0.03430.2973-0.07340.259532.942863.3606-22.216
80.64150.0792-0.18221.67341.90973.89720.06770.0671-0.0655-0.1965-0.12350.0341-0.4326-0.29010.06820.25280.0217-0.00580.1782-0.03650.222532.781369.6301-10.2789
90.33790.2190.11335.11823.39593.9860.0071-0.0233-0.1364-0.4887-0.47630.5307-0.5789-1.00150.36290.30720.1454-0.0920.4049-0.0970.330324.393470.4889-14.0913
103.0771-0.3014-0.35761.5362-0.20152.87840.1031-0.3247-0.4107-0.1195-0.0369-0.17660.27330.7351-0.09410.18820.04790.00640.36740.07870.328747.722664.882522.0711
110.63470.380.90190.9288-0.13971.8242-0.0836-0.1641-0.4509-0.16940.25820.10650.4030.62080.1750.25640.16480.06960.4715-0.04630.419252.092658.40482.1299
122.9449-0.0462-0.89982.48260.92744.2760.11820.13250.0076-0.51340.1414-0.2305-0.62960.1987-0.16240.3487-0.05450.08010.2375-0.07990.245445.305770.0023-17.9554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 17 )H2 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 45 )H18 - 45
3X-RAY DIFFRACTION3chain 'H' and (resid 46 through 65 )H46 - 65
4X-RAY DIFFRACTION4chain 'H' and (resid 66 through 92 )H66 - 92
5X-RAY DIFFRACTION5chain 'H' and (resid 93 through 110 )H93 - 110
6X-RAY DIFFRACTION6chain 'H' and (resid 111 through 131 )H111 - 131
7X-RAY DIFFRACTION7chain 'H' and (resid 132 through 146 )H132 - 146
8X-RAY DIFFRACTION8chain 'H' and (resid 147 through 202 )H147 - 202
9X-RAY DIFFRACTION9chain 'H' and (resid 203 through 228 )H203 - 228
10X-RAY DIFFRACTION10chain 'L' and (resid 2 through 110 )L2 - 110
11X-RAY DIFFRACTION11chain 'L' and (resid 111 through 123 )L111 - 123
12X-RAY DIFFRACTION12chain 'L' and (resid 124 through 220 )L124 - 220

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