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- PDB-8ee5: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ11... -

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Basic information

Entry
Database: PDB / ID: 8ee5
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ119-D in complex with ZIKV E glycoprotein
Components
  • Envelope protein E
  • rhMZ119-D antibody heavy chain
  • rhMZ119-D antibody light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ZIKV / ZIKV-specific / cross-protomer epitopes / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / centrosome / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesZika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.583 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 6, 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 / 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
Z: Envelope protein E
H: rhMZ119-D antibody heavy chain
L: rhMZ119-D antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5084
Polymers90,0843
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Migrated as complex of Fab (heavy and light chain) and ZIKVE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.681, 103.672, 196.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Envelope protein E


Mass: 44214.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A024B7W1
#2: Antibody rhMZ119-D antibody heavy chain


Mass: 23296.004 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: Antibody rhMZ119-D antibody light chain


Mass: 22573.865 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)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.06M Nitrate Phosphate Sulfate , 0.1M Sodium HEPES and MOPS (acid) pH 7.5, 20% Ethylene glycol, 10 % PEG 8000 + 2% w/v Benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.58→29.4 Å / Num. obs: 23586 / % possible obs: 98.6 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rrim(I) all: 0.21 / Rsym value: 0.2 / Net I/σ(I): 9.97
Reflection shellResolution: 3.58→3.72 Å / Num. unique obs: 1900 / CC1/2: 0.84

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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: 6NIP

6nip


Resolution: 3.583→14.994 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 1176 4.99 %
Rwork0.249 --
obs0.2513 23586 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.583→14.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 28 0 6300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036414
X-RAY DIFFRACTIONf_angle_d0.688740
X-RAY DIFFRACTIONf_dihedral_angle_d11.5483826
X-RAY DIFFRACTIONf_chiral_restr0.054996
X-RAY DIFFRACTIONf_plane_restr0.0041112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.583-3.74340.35141490.33062757X-RAY DIFFRACTION97
3.7434-3.93740.37841430.31612792X-RAY DIFFRACTION100
3.9374-4.17910.33731470.2912790X-RAY DIFFRACTION100
4.1791-4.49370.30581450.24852813X-RAY DIFFRACTION100
4.4937-4.93130.30361450.23242817X-RAY DIFFRACTION100
4.9313-5.61180.31191460.23282825X-RAY DIFFRACTION100
5.6118-6.9510.28311480.26982820X-RAY DIFFRACTION100
6.951-14.9940.23021530.19722796X-RAY DIFFRACTION100
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)
1-0.09270.07620.49220.5542-0.23934.667-0.02510.10360.0681-0.0624-0.03770.00220.3418-0.2014-0.01170.5595-0.08080.01610.90220.06210.8765-65.33219.689193.926
21.0721-0.35582.38930.6826-0.217111.3634-0.1071-0.0925-0.2595-0.08180.11060.00150.0303-0.364-0.07720.6444-0.05740.07790.9179-0.07870.9947-69.97219.264179.425
34.8013-0.3504-1.21633.587-2.48428.3426-0.14670.3525-0.1811-0.65890.14970.11060.7952-0.24230.34820.8246-0.1721-0.09320.6729-0.07930.6782-61.96918.265137.434
43.3335-0.1334-1.31766.01520.31561.0851.2864-0.32690.0766-0.6245-0.5429-0.38370.0488-0.7935-0.07680.8450.0125-0.1850.9742-0.04141.0595-54.85359.408207.41
53.83750.1509-1.31843.4857-1.07531.9745-0.54090.4581-0.2384-0.83921.2312-0.14910.8787-0.19720.25810.7178-0.0219-0.15150.9432-0.09640.81-55.844.796204.921
60.8191-0.7450.14380.8972-1.51870.9677-0.10811.5983-0.21250.18760.7333-1.7812-0.83741.2425-0.35120.41610.2545-0.10370.5689-0.14630.4493-59.08648.928217.29
70.10040.10020.05270.1112-0.07810.05460.427-1.152-0.0926-0.6701-0.6830.1187-0.26530.0215-00.9637-0.0276-0.20520.55560.13181.1051-61.38754.595209.558
80.04080.1081-0.1281-0.036-0.05880.0884-0.76460.51750.12790.53120.62011.33940.01720.8075-00.91340.0923-0.13371.0145-0.05550.8054-52.17745.038214.189
93.69273.5673-0.46533.2107-0.93061.2880.05950.10630.518-1.2727-0.1045-1.6435-0.2852-0.0680.25170.70240.2516-0.01941.01350.15050.7635-49.19653.38211.89
100.14880.4165-0.56691.7368-0.68041.3512-0.5589-0.05810.41041.0347-0.0802-0.0635-2.17640.04450.28381.7187-0.1363-0.13761.31770.11920.8552-37.64884.383212.671
118.76542.77234.98536.9995-0.78343.9054-0.26993.36520.4156-1.41-0.54040.99720.10162.11280.89041.4943-0.2004-0.19461.2665-0.34330.938-39.3379.509211.862
120.8677-2.7877-1.32548.67654.21222.04310.2267-2.2617-0.1693-1.6684-0.4722-1.0108-1.5188-0.63860.57611.6782-0.54430.24331.947-0.17320.9991-31.80876.486202.958
133.34640.58880.25574.22472.10217.2167-0.04050.96850.3676-1.1411.31360.9458-2.21150.9908-0.28071.34430.3038-0.01060.56140.2371.0047-39.60475.054215.336
142.01844.3227-7.7034.1849-2.23975.1792-0.26861.4432.9891-0.91020.48-1.1043-0.62572.419-0.07741.1261-0.21840.2052.2415-0.10621.1525-25.16680.795210.496
150.4777-0.66710.10271.21491.69247.2218-0.19890.94931.0399-0.5357-0.2208-0.4574-0.28551.16230.69271.5233-0.36270.01871.86250.57441.2282-35.1182.672202.645
162.09094.05094.25071.15890.0911.0459-1.8538-2.41471.82313.0371-1.90926.140.4571-4.23910.66340.1830.7271-1.83940.23770.8938-2.2527-38.9347.952232.314
170.65360.17460.42060.10540.10520.41870.40570.0094-0.0819-3.1943-0.7617-1.00930.0553-0.22820-0.4144-0.2973-0.14220.2398-0.12990.1847-40.69340.626222.872
18-3.27881.38671.15451.0367-1.2173-0.70761.8643-1.77122.00680.878-1.15250.3179-2.83260.274-0.0011-1.5408-0.9823-0.4155-0.3432-0.33950.8968-37.65849.864226.101
193.63461.8752-0.70732.87851.89933.1015-0.09880.19390.1990.11890.28070.4514-0.223-0.1144-0.13490.6977-0.0673-0.09291.03110.04460.8385-34.42982.194225.356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN Z AND RESID 1:129 )Z1 - 129
2X-RAY DIFFRACTION2( CHAIN Z AND RESID 130:304 )Z130 - 304
3X-RAY DIFFRACTION3( CHAIN Z AND RESID 305:403 )Z305 - 403
4X-RAY DIFFRACTION4( CHAIN H AND RESID 1:17 )H1 - 17
5X-RAY DIFFRACTION5( CHAIN H AND RESID 18:33 )H18 - 33
6X-RAY DIFFRACTION6( CHAIN H AND RESID 34:69 )H34 - 69
7X-RAY DIFFRACTION7( CHAIN H AND RESID 70:87 )H70 - 87
8X-RAY DIFFRACTION8( CHAIN H AND RESID 88:100 )H88 - 100
9X-RAY DIFFRACTION9( CHAIN H AND RESID 101:111 )H101 - 111
10X-RAY DIFFRACTION10( CHAIN H AND RESID 112:133 )H112 - 133
11X-RAY DIFFRACTION11( CHAIN H AND RESID 134:148 )H134 - 148
12X-RAY DIFFRACTION12( CHAIN H AND RESID 149:158 )H149 - 158
13X-RAY DIFFRACTION13( CHAIN H AND RESID 159:176 )H159 - 176
14X-RAY DIFFRACTION14( CHAIN H AND RESID 177:187 )H177 - 187
15X-RAY DIFFRACTION15( CHAIN H AND RESID 188:211 )H188 - 211
16X-RAY DIFFRACTION16( CHAIN L AND RESID 1:18 )L1 - 18
17X-RAY DIFFRACTION17( CHAIN L AND RESID 19:61 )L19 - 61
18X-RAY DIFFRACTION18( CHAIN L AND RESID 62:119 )L62 - 119
19X-RAY DIFFRACTION19( CHAIN L AND RESID 120:210 )L120 - 210

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