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- PDB-7a3q: Crystal structure of dengue 4 virus envelope glycoprotein in comp... -

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Basic information

Entry
Database: PDB / ID: 7a3q
TitleCrystal structure of dengue 4 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10
Components
  • (Single Chain Variable ...) x 2
  • Envelope protein E
KeywordsVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / DENGUE / Antibody
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flavivirus envelope glycoprotein E, stem/anchor 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 ...Immunoglobulin-like - #350 / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flavivirus envelope glycoprotein E, stem/anchor 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-3CX / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 4
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 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
A: Envelope protein E
B: Envelope protein E
H: Single Chain Variable Fragment
I: Single Chain Variable Fragment
L: Single Chain Variable Fragment
M: Single Chain Variable Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,21210
Polymers149,2956
Non-polymers9174
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, envelope protein (Chain A and B) are present as dimers on virion surface and in the crystallographic asymmetric unit. Chain H/I (antibody heavy chain fragment) forms a ...Evidence: gel filtration, envelope protein (Chain A and B) are present as dimers on virion surface and in the crystallographic asymmetric unit. Chain H/I (antibody heavy chain fragment) forms a heterodimer with chain L/M (antibody light chain fragment) .
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-29 kcal/mol
Surface area55890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.985, 133.180, 93.536
Angle α, β, γ (deg.)90.000, 92.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HILM

#2: Antibody Single Chain Variable Fragment


Mass: 15679.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: variable domain from the heavy chain 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 Single Chain Variable Fragment


Mass: 15632.767 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: variable domain from the light chain of broadly neutralising antibody EDE1 C10
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Envelope protein E / Matrix protein / Small envelope protein M


Mass: 43335.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DENGUE VIRUS SEROTYPE 4 ENVELOPE PROTEIN ECTODOMAIN
Source: (gene. exp.) Dengue virus 4 / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: S5S2D1
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 42 molecules

#5: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100 mM CAPSO pH 9.6, 16.7% (w/v) PEG 8,000, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.254 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 43980 / % possible obs: 99.1 % / Redundancy: 3.19 % / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4614 / CC1/2: 0.688 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UAJ, 3FKU

3uaj

3fku


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9158 / SU R Cruickshank DPI: 0.731 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.618 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 2204 5.03 %RANDOM
Rwork0.216 ---
obs0.2171 43818 99.01 %-
Displacement parametersBiso max: 181.89 Å2 / Biso mean: 81.58 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.8694 Å20 Å2-3.6286 Å2
2---2.4601 Å20 Å2
3---1.5907 Å2
Refine analyzeLuzzati coordinate error obs: 0.503 Å
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 58 40 9449
Biso mean--110.79 49.38 -
Num. residues----1212
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3292SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes205HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1393HARMONIC5
X-RAY DIFFRACTIONt_it9628HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1259SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9507SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9628HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg13048HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion1.91
X-RAY DIFFRACTIONt_other_torsion18.79
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3273 177 5.51 %
Rwork0.2732 3038 -
all0.2761 3215 -
obs--99.01 %
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)
13.89172.5235-2.86831.115-2.25332.5528-0.0077-0.0213-0.15410.0401-0.10670.00690.3036-0.01490.11440.1434-0.04550.1466-0.2093-0.04110.06117.1008-47.9785316.1767
21.47712.3208-2.95041.5978-2.82532.3229-0.00190.17930.1511-0.06420.1917-0.06880.0326-0.0295-0.1898-0.0850.05570.11970.24690.15420.0353132.84620.6396273.04
31.67773.0172-2.90151.2215-2.78953.5098-0.04160.0279-0.1551-0.18850.04140.00960.0027-0.03370.00010.00610.07820.1384-0.02330.05640.1299147.7705-21.6238285.2806
40.61852.3105-3.08220-2.82574.96930.06030.04340.07870.1296-0.045-0.10440.0892-0.0725-0.01520.2869-0.02090.1628-0.08090.08510.0105110.3268-19.587312.3729
52.9460.213-2.21574.5264-1.71665.7005-0.0148-0.03740.0852-0.00320.01930.2375-0.0683-0.2121-0.0045-0.1129-0.13790.0678-0.03380.1043-0.084987.7877-45.6614335.8619
62.97181.0399-0.94585.3129-1.55622.2458-0.02110.17450.2131-0.0974-0.0483-0.0990.01530.0840.0695-0.0279-0.05570.0854-0.06850.0309-0.1049163.1193.7784256.2079
70.0320.03030.01850.027-0.01750.04010.0002-0.00210.00060.0014-0.0005-0.001-0.0002-0.00040.00030.01970.0157-0.00980.02880.00040.033154.0695-18.1628300.9649
80.00020.0013-0.00310.0267-0.0010.00860.0004-0.00050.00110.001-0.00030.0006-0.0011-0.0006-0.00010.01060.0038-0.00680.01560.00060.0224122.8142-11.8942320.2989
93.36270.3325-0.49822.20080.71944.9762-0.1319-0.43990.26380.112-0.0462-0.0404-0.2324-0.19460.1781-0.15310.1192-0.0138-0.08710.0006-0.1114161.15582.7921290.9607
102.7391-0.2985-0.21622.5310.87881.8288-0.1212-0.4030.23460.08940.4239-0.4497-0.16290.3105-0.3027-0.0511-0.13070.1512-0.0772-0.157-0.0498114.2642-22.7507340.8767
110.0008-0.0214-0.01110.0064-0.0095-0.0008-0.0009-0.0108-0.00490.00470.0009-0.00380.00290.00430-0.00290.0188-0.00540.0094-0.03460.0089175.97331.3344298.8772
12-0.00110.01060.013300.02190.04680.00010.0010.0078-0.0026-0.0005-0.0014-0.0073-0.00190.00040.01290.0109-0.00360.001-0.0204-0.001110.706-8.3485348.9979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1tls3_dom1A0
2X-RAY DIFFRACTION2tls3_dom1B0
3X-RAY DIFFRACTION3tls2_dom2tipA0
4X-RAY DIFFRACTION4tls2_dom2tipB0
5X-RAY DIFFRACTION5tls1_dom3A0
6X-RAY DIFFRACTION6tls1_dom3B0
7X-RAY DIFFRACTION7tls1_sugarsA-10
8X-RAY DIFFRACTION8tls1_sugarsB-10
9X-RAY DIFFRACTION9tls1_scFvU0
10X-RAY DIFFRACTION10tls1_scFvV0
11X-RAY DIFFRACTION11tls1_3CX-U0
12X-RAY DIFFRACTION12tls1_3CX-V0

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