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- PDB-8ef0: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ104-D -

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Basic information

Entry
Database: PDB / ID: 8ef0
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ104-D
Components
  • rhMZ104-D antibody heavy chain
  • rhMZ104-D 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: 2.55 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 1.1Nov 6, 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: rhMZ104-D antibody heavy chain
L: rhMZ104-D antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3066
Polymers48,0142
Non-polymers2914
Water2,144119
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 area3920 Å2
ΔGint-114 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.728, 71.728, 159.991
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11H-455-

HOH

21H-457-

HOH

31L-426-

HOH

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Components

#1: Antibody rhMZ104-D antibody heavy chain


Mass: 24472.354 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 rhMZ104-D antibody light chain


Mass: 23542.021 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 26% PEG 8K, 0.2M ZnAc, 0.1M Tris-HCl (pH8.5)

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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 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 17381 / % possible obs: 98.4 % / Redundancy: 5.9 % / CC1/2: 0.81 / Rsym value: 0.194 / Net I/σ(I): 9.2
Reflection shellResolution: 2.48→2.56 Å / Num. unique obs: 1540 / CC1/2: 0.46 / Rsym value: 0.96 / % possible all: 89.1

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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: 2.55→9.947 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 723 5.06 %
Rwork0.1847 13568 -
obs0.1876 14291 89.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.52 Å2 / Biso mean: 43.5236 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: final / Resolution: 2.55→9.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 8 119 3457
Biso mean--107.17 36.35 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053421
X-RAY DIFFRACTIONf_angle_d0.8174664
X-RAY DIFFRACTIONf_chiral_restr0.047515
X-RAY DIFFRACTIONf_plane_restr0.005596
X-RAY DIFFRACTIONf_dihedral_angle_d8.7832034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5501-2.74320.32171030.24821822192561
2.7432-3.01220.29681480.22722706285491
3.0122-3.43230.26741560.19892969312599
3.4323-4.26680.21561560.16752986314299
4.2668-9.9470.20541600.16243085324598
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)
12.88611.1969-0.67363.5552-1.01281.49120.1579-0.20940.3704-0.1373-0.03140.5083-0.3364-0.6394-0.10390.25730.2083-0.04030.42720.00310.30480.88357.5067.975
22.20160.25290.15991.29411.22552.1816-0.0403-0.19110.5271-0.95170.6430.1831-1.1053-0.2870.98750.00460.2746-0.06990.27890.02680.25757.94254.42312.898
34.48790.62190.7484.12811.13393.0246-0.4202-0.1599-0.3910.42420.26790.0685-0.02680.74440.13840.21310.06670.0030.47970.11970.289916.31535.16329.354
43.5122-0.1809-0.83961.1894-0.62981.864-0.03130.19910.26830.1544-0.04030.2013-0.03330.06180.17260.08010.01180.02760.28340.14630.3411.91934.86928.284
54.3893-1.6073-0.53494.9298-0.1621.9666-0.05490.26170.31550.14960.0595-0.3137-0.25510.07720.190.262-0.02810.01450.18560.06710.213127.69757.6162.163
63.4501-0.5782-0.962.4011-0.1611.90720.08010.02990.9536-0.18060.0408-0.1466-0.62460.07660.14850.5222-0.0003-0.11120.24780.00690.320221.82665.6760.444
73.2235-0.8885-0.78382.52260.5140.8831-0.1217-0.54260.86530.31330.0349-0.539-0.62780.0837-0.10950.61170.0014-0.1550.2187-0.0770.508624.66167.9648.156
85.8542-0.373-0.17823.7689-0.20081.4002-0.4963-0.47830.32480.62590.1242-0.0797-0.6017-0.14180.2220.43850.0549-0.05330.2113-0.0670.229823.84960.319.385
95.553-0.5804-0.14283.8460.05861.2076-0.24560.6037-0.0178-0.02520.00870.3925-0.439-0.12160.11750.29780.0356-0.12310.2345-0.00880.22618.06459.1242.708
103.51890.3396-0.98383.2739-1.02622.1851-0.3039-0.0374-0.42920.1359-0.01640.25310.0684-0.07880.32190.15480.06830.03880.28740.07410.291422.55829.80423.227
113.49351.697-1.01351.65440.46811.430.02520.6678-0.9099-0.0667-0.211-0.47520.2170.14180.28460.08910.0625-0.03910.3717-0.03550.442230.13830.08915.271
124.82520.7249-0.59793.9041-0.67334.1627-0.10360.3772-0.2039-0.07050.16490.5615-0.0031-0.1380.08160.14910.05520.04270.33620.00520.286123.34431.04116.244
132.75530.3729-0.45642.6775-0.69211.6113-0.4978-0.3783-1.74390.40970.19990.42960.84650.060.43360.33040.17910.29110.18950.22651.052624.29118.13921.148
141.34991.7523-0.48563.1383-0.83653.2956-0.6134-0.2669-0.4643-0.2158-0.14-0.5711-0.05090.6318-0.3857-0.0093-0.08280.15270.3090.28890.438732.16825.32922.344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:99 )H2 - 99
2X-RAY DIFFRACTION2( CHAIN H AND RESID 100:138 )H100 - 138
3X-RAY DIFFRACTION3( CHAIN H AND RESID 139:179 )H139 - 179
4X-RAY DIFFRACTION4( CHAIN H AND RESID 180:213 )H180 - 213
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:17 )L1 - 17
6X-RAY DIFFRACTION6( CHAIN L AND RESID 18:40 )L18 - 40
7X-RAY DIFFRACTION7( CHAIN L AND RESID 41:83 )L41 - 83
8X-RAY DIFFRACTION8( CHAIN L AND RESID 84:100 )L84 - 100
9X-RAY DIFFRACTION9( CHAIN L AND RESID 101:115 )L101 - 115
10X-RAY DIFFRACTION10( CHAIN L AND RESID 116:149 )L116 - 149
11X-RAY DIFFRACTION11( CHAIN L AND RESID 150:160 )L150 - 160
12X-RAY DIFFRACTION12( CHAIN L AND RESID 161:191 )L161 - 191
13X-RAY DIFFRACTION13( CHAIN L AND RESID 192:207 )L192 - 207
14X-RAY DIFFRACTION14( CHAIN L AND RESID 208:208 )L208

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