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- PDB-8eez: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ100-C -

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Basic information

Entry
Database: PDB / ID: 8eez
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ100-C
Components
  • rhMZ100-C antibody heavy chain
  • rhMZ100-C antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV / ZIKV-specific / cross-protomer epitopes / VIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: rhMZ100-C antibody heavy chain
L: rhMZ100-C antibody light chain


Theoretical massNumber of molelcules
Total (without water)46,7322
Polymers46,7322
Non-polymers00
Water2,630146
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 area3280 Å2
ΔGint-19 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.981, 71.226, 114.176
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 rhMZ100-C antibody heavy chain


Mass: 23274.891 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 rhMZ100-C antibody light chain


Mass: 23456.941 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.: 146 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22.5% PEG 4K, 22.5% IPA, 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: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 22274 / % possible obs: 92.5 % / Redundancy: 4.1 % / CC1/2: 0.99 / Net I/σ(I): 7.6
Reflection shellResolution: 2.19→2.26 Å / Num. unique obs: 1968 / CC1/2: 0.579

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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: 4FQQ

4fqq


Resolution: 2.25→14.896 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 966 5 %
Rwork0.1855 18344 -
obs0.1879 19310 86.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.26 Å2 / Biso mean: 39.6002 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.25→14.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 146 3370
Biso mean---40.31 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093301
X-RAY DIFFRACTIONf_angle_d1.1964501
X-RAY DIFFRACTIONf_chiral_restr0.064509
X-RAY DIFFRACTIONf_plane_restr0.009580
X-RAY DIFFRACTIONf_dihedral_angle_d7.9261966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2502-2.36840.30241170.22782220233775
2.3684-2.51610.28131190.22732259237876
2.5161-2.70930.29111250.22832375250080
2.7093-2.980.25381440.20972747289191
2.98-3.40670.23751530.19252878303195
3.4067-4.27510.20071520.16132903305595
4.2751-14.89590.21321560.16582962311894
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)
10.0419-0.0337-0.00670.08060.0160.07160.00630.0835-0.09250.08670.01430.0848-0.11140.1281-00.14240.01820.0040.1444-0.01670.14922.547352.4524-9.1335
25.1076-1.2018-0.6391.2218-1.75763.9475-0.0088-0.45720.77460.74140.3453-0.4226-0.17690.1002-0.19340.3495-0.0578-0.00420.2399-0.01630.462-0.974455.125930.8515
33.6368-0.27650.09955.43233.0096.48950.1463-0.14170.24530.1516-0.2150.3451-0.1586-0.30080.04380.16070.0017-0.00470.18830.02370.2737-6.899751.239428.1303
4-0.00050.0056-0.0065-0.004-0.02270.0071-0.2283-0.10780.0858-0.02560.1157-0.1513-0.23910.1154-00.2137-0.0293-0.02040.26270.01530.24475.916576.6599-1.7775
5-0.00270.01060.00840.00480.01530.0087-0.11150.0629-0.0221-0.0167-0.03610.0384-0.04340.0343-00.1966-0.06290.00510.1635-0.03210.1521-2.101670.399-7.4875
60.005-0.0084-0.00330.0063-0.01280.01350.03420.0530.069-0.04170.1285-0.0247-0.1758-0.138800.2369-0.13460.05680.10240.1920.0233-0.267979.6007-9.3199
7-0.00210.0049-0.00260.00480.01760.011-0.00930.0293-0.0867-0.06450.2317-0.0302-0.0827-0.1874-00.2277-0.00260.03870.2364-0.06090.1354-3.456372.2297-2.3651
80.501-0.06150.27330.3471-0.42540.5044-0.2775-0.7112-0.02620.44340.0306-0.2737-0.2061-0.41620.14360.00480.01940.1092-0.175-0.05220.14880.233268.722711.8963
95.0523-1.29961.62753.0995-1.53584.84780.1391-0.2366-0.06330.0508-0.06440.0769-0.0458-0.0941-0.0840.3483-0.02780.01610.1208-0.06390.21174.54561.169724.461
102.0156-1.0412.21322.5132-1.06964.04510.17850.3030.0335-0.1714-0.06980.2139-0.2066-0.0689-0.06850.37880.03260.01650.2232-0.04610.32281.352364.262818.2546
115.7343-1.62831.97011.05230.42042.2380.0204-0.10760.05830.0294-0.0137-0.1055-0.1205-0.0011-0.01560.2969-0.07580.05250.17080.03290.23299.404464.296825.6462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 114 )H2 - 114
2X-RAY DIFFRACTION1chain 'H' and (resid 2 through 111 )H2 - 111
3X-RAY DIFFRACTION2chain 'H' and (resid 112 through 143 )H112 - 143
4X-RAY DIFFRACTION3chain 'H' and (resid 144 through 210 )H144 - 210
5X-RAY DIFFRACTION4chain 'L' and (resid 2 through 32 )L2 - 32
6X-RAY DIFFRACTION5chain 'L' and (resid 33 through 52 )L33 - 52
7X-RAY DIFFRACTION6chain 'L' and (resid 53 through 75 )L53 - 75
8X-RAY DIFFRACTION7chain 'L' and (resid 76 through 92 )L76 - 92
9X-RAY DIFFRACTION8chain 'L' and (resid 93 through 121 )L93 - 121
10X-RAY DIFFRACTION9chain 'L' and (resid 122 through 150 )L122 - 150
11X-RAY DIFFRACTION10chain 'L' and (resid 151 through 171 )L151 - 171
12X-RAY DIFFRACTION11chain 'L' and (resid 172 through 209 )L172 - 209

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