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- PDB-7a3n: Crystal structure of Zika virus envelope glycoprotein in complex ... -

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Basic information

Entry
Database: PDB / ID: 7a3n
TitleCrystal structure of Zika virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C10
Components
  • (EDE1 C10 Fab) x 2
  • Core protein
KeywordsVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / ANTIBODY / Fab / IMMUNOCOMPLEX / ZIKA / broadly neutralising antibody
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / symbiont entry into host cell / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule 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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSharma, A. / Vaney, M.C. / Guardado-Calvo, P. / Duquerroy, S. / Rouvinski, A. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
Wellcome Trust France
Citation
Journal: Cell / Year: 2021
Title: The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.
Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado- ...Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado-Calvo / Ahmed Haouz / Patrick England / Ren Sun / Z Hong Zhou / Juthathip Mongkolsapaya / Gavin R Screaton / Felix A Rey /
Abstract: The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative ...The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.
#1: Journal: Nature / Year: 2016
Title: Structural basis of potent Zika-dengue virus antibody cross-neutralization.
Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. ...Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. / Mongkolsapaya, J. / Heinz, F.X. / Screaton, G.R. / Rey, F.A.
#2: Journal: Nature / Year: 2015
Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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
A: Core protein
H: EDE1 C10 Fab
L: EDE1 C10 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9674
Polymers96,9273
Non-polymers401
Water5,621312
1
A: Core protein
H: EDE1 C10 Fab
L: EDE1 C10 Fab
hetero molecules

A: Core protein
H: EDE1 C10 Fab
L: EDE1 C10 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9358
Polymers193,8556
Non-polymers802
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area4550 Å2
ΔGint-30 kcal/mol
Surface area37860 Å2
Unit cell
Length a, b, c (Å)53.964, 168.610, 220.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-762-

HOH

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Components

#1: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 45138.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZIKA virus envelope protein ectodomain / Source: (gene. exp.) Zika virus / Gene: GP1, BKC09_64228gpGP1 / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: A0A1U9YHM2, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Antibody EDE1 C10 Fab


Mass: 28989.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heavy chain from the Fab fragment of broadly neutralising antibody EDE1 C10
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody EDE1 C10 Fab


Mass: 22800.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Light chain from the Fab fragment of broadly neutralising antibody EDE1 C10
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.59 Å3/Da / Density % sol: 52.48 % / Description: Rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Imidazole (pH 8), 10% PEG 8,000, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.99→46.58 Å / Num. obs: 68764 / % possible obs: 98.9 % / Redundancy: 7.8 % / CC1/2: 0.954 / Rmerge(I) obs: 0.664 / Net I/σ(I): 5.3
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 3874 / CC1/2: 0.111

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHENIX1.17.1_3660phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LBV, 4UT9

5lbv

4ut9


Resolution: 2.1→19.91 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1722 2.91 %
Rwork0.2034 57424 -
obs0.2045 59146 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.83 Å2 / Biso mean: 52.6209 Å2 / Biso min: 17.15 Å2
Refinement stepCycle: final / Resolution: 2.1→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 1 312 6534
Biso mean--40.67 44.69 -
Num. residues----821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.160.32751430.329747524895
2.16-2.230.34121400.319946844824
2.23-2.310.361420.309847194861
2.31-2.40.29881420.286947564898
2.4-2.510.32111430.271647324875
2.51-2.640.2931410.259447424883
2.64-2.810.27981440.23647594903
2.81-3.030.25091440.213447974941
3.03-3.330.23551420.192647714913
3.33-3.810.21591450.160648234968
3.81-4.790.1731450.138648494994
4.79-19.910.19911510.174450405191
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)
12.1864-0.48543.71320.0673-0.61916.2430.00970.0850.0108-0.0174-0.07110.01190.07530.11490.08040.1462-0.03410.00720.26880.03530.24037.6406-19.734543.8632
24.01310.16114.17360.28030.01395.94960.00310.2702-0.27850.06230.0209-0.12210.00210.48570.00370.19840.06270.01720.2774-0.03420.3154-2.0291-19.819216.0077
32.3278-0.60460.14021.5724-0.40353.72150.0932-0.17150.22980.02320.00780.1312-0.4285-0.7299-0.0780.19370.02350.01480.45310.02380.32859.3781-18.295950.6849
44.1759-0.0425-0.51231.43130.49511.90270.00540.6581-0.1941-0.171-0.08640.1842-0.053-0.34960.06450.20670.0274-0.01050.3485-0.03870.2432-27.3757-19.28935.3101
52.34870.16021.26384.2752-1.28772.60720.2654-0.1219-0.44190.5391-0.0435-0.64290.53140.4191-0.09660.44870.0992-0.18960.256-0.03580.4425-13.7632-46.925231.5622
61.7288-0.7190.36366.5233-2.49412.3450.3103-0.006-0.39870.4743-0.1281-0.63510.39250.25050.05020.37690.0457-0.19370.2579-0.05850.3345-16.8163-45.515627.8807
74.87811.91581.29134.8360.19083.61710.25540.0291-0.86821.177-0.1211-0.7676-0.2633-0.0491-0.15180.83410.0469-0.17780.38350.01510.8336-31.0391-80.610133
82.52731.42550.71062.41811.15491.81120.18610.1048-0.20740.0358-0.1184-0.02820.3867-0.321-0.01560.308-0.0185-0.0610.2076-0.06310.2323-33.0985-43.958719.8372
92.86530.60450.06342.9199-2.62262.62140.0628-0.759-0.22941.13950.08570.23091.0253-0.5877-0.13491.2818-0.06080.05020.5646-0.04010.4239-41.6356-68.449936.1867
105.5340.30990.01452.1472-3.73756.8597-0.2352-0.64720.01991.50540.17510.2870.4479-0.85640.0571.4335-0.10130.0820.4747-0.11120.5718-42.2795-67.728236.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )A1 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 208 )A130 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 278 )A209 - 278
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 403 )A279 - 403
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 96 )H1 - 96
6X-RAY DIFFRACTION6chain 'H' and (resid 97 through 119 )H97 - 119
7X-RAY DIFFRACTION7chain 'H' and (resid 120 through 213 )H120 - 213
8X-RAY DIFFRACTION8chain 'L' and (resid 3 through 106A)L3 - 106
9X-RAY DIFFRACTION9chain 'L' and (resid 107 through 161 )L107 - 161
10X-RAY DIFFRACTION10chain 'L' and (resid 162 through 206 )L162 - 206

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