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- PDB-7a3t: Crystal structure of dengue 3 virus envelope glycoprotein in comp... -

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Basic information

Entry
Database: PDB / ID: 7a3t
TitleCrystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
Components
  • (EDE1 C8 antibody Fab ...) x 2
  • Core proteinCapsid
KeywordsVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / DENGUE / Antibody
Function / homology
Function and homology information


: / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 ...: / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDengue virus 3
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein
H: EDE1 C8 antibody Fab fragment
L: EDE1 C8 antibody Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,28812
Polymers99,6413
Non-polymers1,6479
Water1448
1
A: Core protein
hetero molecules

A: Core protein
hetero molecules

H: EDE1 C8 antibody Fab fragment
L: EDE1 C8 antibody Fab fragment
hetero molecules

H: EDE1 C8 antibody Fab fragment
L: EDE1 C8 antibody Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,57624
Polymers199,2816
Non-polymers3,29518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
crystal symmetry operation6_445-x-1,-x+y-1,-z+1/31
Buried area19860 Å2
ΔGint-210 kcal/mol
Surface area74520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.309, 110.309, 217.337
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody EDE1 C8 antibody Fab fragment


Mass: 28882.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heavy chain from the Fab fragment of EDE1 C8 antibody
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody EDE1 C8 antibody Fab fragment


Mass: 23998.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Light chain from the Fab fragment of EDE1 C8 antibody
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, 2 molecules A

#1: Protein Core protein / Capsid / 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: 46759.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DENGUE VIRUS SEROTYPE 3 ENVELOPE PROTEIN ECTODOMAIN
Source: (gene. exp.) Dengue virus 3 / Gene: POLY / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: A0A481XTQ0, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 16 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM Na3 Citrate pH 5.6, 15% w/v PEG 4,000, 200 mM (NH4)2 SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→49.15 Å / Num. obs: 44949 / % possible obs: 99.5 % / Redundancy: 11.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.32 / Net I/σ(I): 5.1
Reflection shellResolution: 2.65→2.75 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4497 / CC1/2: 0.095 / % possible all: 95.8

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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: D_1292109938 and 4UTA

4uta


Resolution: 2.65→29.53 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2029 6.11 %
Rwork0.2067 31173 -
obs0.2096 33202 74.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.32 Å2 / Biso mean: 70.8222 Å2 / Biso min: 26.36 Å2
Refinement stepCycle: final / Resolution: 2.65→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 104 8 6381
Biso mean--105.54 45.18 -
Num. residues----818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.66-2.720.4854150.3972602759
2.72-2.80.3878370.350753357018
2.8-2.880.4092600.357183389328
2.88-2.970.3376720.36131102117437
2.97-3.080.37811010.33731550165153
3.08-3.20.37751680.31762576274487
3.2-3.350.32141950.289230013196100
3.35-3.520.31631900.260129773167100
3.52-3.740.3241960.236730123208100
3.74-4.030.24431930.192329983191100
4.03-4.440.20381980.158430383236100
4.44-5.080.17511970.1530223219100
5.08-6.380.24051960.186530743270100
6.39-29.530.23072110.187331973408100
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)
10.41410.2028-0.86060.405-0.05366.2653-0.06160.1658-0.05150.19650.0938-0.03210.54860.361-0.05890.46590.24280.02830.68150.03560.6416-11.8705-49.50213.8794
20.91660.43361.93940.4564-0.45099.93240.17480.2849-0.17720.1525-0.0794-0.51070.72781.0445-0.10740.67310.2772-0.00360.85380.09440.6864-8.7263-49.592528.8869
30.54660.2056-0.01181.4552-0.7162.5742-0.0890.1086-0.0760.32950.2506-0.0588-0.16050.2379-0.15740.51180.28470.11050.9734-0.00710.5801-13.5538-45.1857-2.7544
44.2996-0.3342-0.09011.72220.28242.7297-0.3503-1.0310.00790.59480.1151-0.24080.06520.15890.29431.14310.3422-0.10480.64220.04260.6388-23.5282-48.276857.1523
51.7241-0.17581.14013.8033-0.30662.38540.12210.8561-0.0833-0.11830.0547-0.2420.13311.0639-0.11030.53580.27060.10250.6878-0.08470.4967-25.1114-14.531430.8075
67.45-5.75241.73117.388-1.40124.08860.1842-0.2457-0.6111-0.3540.32350.6057-0.29560.3217-0.56190.41330.08610.08910.36470.00660.4369-30.4346-9.707732.9888
72.0413-0.8141-0.45795.24831.22992.2860.27840.34430.2042-0.1826-0.2142-0.81390.19091.1308-0.25080.49660.26880.10810.5483-0.05050.4029-26.5286-11.431135.8896
82.60510.02130.4991-0.04240.00130.0992-0.385-0.34260.69080.06320.0031-0.12150.9118-0.15640.20111.17390.01710.04390.55910.10570.7369-35.065125.554953.7423
93.175-1.685-0.24633.8878-0.43432.64120.06480.15840.8825-0.21380.0226-0.7627-1.4040.8562-0.08360.9131-0.19110.07660.4930.08820.6964-28.472618.840247.1355
102.8851.54811.97535.81353.4517.8667-0.3516-0.1948-0.13310.8510.19970.8120.70540.37510.0460.59610.17090.01040.28020.01940.5349-35.8603-15.717957.0205
111.2758-0.0481-0.72382.25780.77992.365-0.0851-0.0918-0.26940.49130.2574-0.35150.49850.5167-0.15130.70750.323-0.0250.5134-0.01660.5182-27.4219-20.963753.1416
121.57132.36091.93055.47184.83276.35730.5461-0.23-0.36970.2077-0.7152-0.58330.54380.4525-0.13710.6790.42190.01630.2967-0.07420.518-30.1319-17.047449.8655
133.2207-1.39781.33452.2808-0.79842.18480.09240.32880.4668-0.3316-0.16770.1266-0.44120.04410.02670.81410.08880.00990.2769-0.00780.4891-41.832513.274854.1648
143.3683-2.07571.23384.154-2.53453.0744-0.04440.06390.5213-0.04720.04520.2338-0.95610.021-0.01120.90360.0691-0.00330.2993-0.05820.4834-43.981416.200255.2253
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 212 )A130 - 212
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 279 )A213 - 279
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 396 )A280 - 396
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 82 )H1 - 82
6X-RAY DIFFRACTION6chain 'H' and (resid 82A through 96 )H82
7X-RAY DIFFRACTION7chain 'H' and (resid 97 through 119 )H97 - 119
8X-RAY DIFFRACTION8chain 'H' and (resid 120 through 134 )H120 - 134
9X-RAY DIFFRACTION9chain 'H' and (resid 135 through 213 )H135 - 213
10X-RAY DIFFRACTION10chain 'L' and (resid 0 through 25 )L0 - 25
11X-RAY DIFFRACTION11chain 'L' and (resid 26 through 75 )L26 - 75
12X-RAY DIFFRACTION12chain 'L' and (resid 76 through 102 )L76 - 102
13X-RAY DIFFRACTION13chain 'L' and (resid 103 through 163 )L103 - 163
14X-RAY DIFFRACTION14chain 'L' and (resid 164 through 213 )L164 - 213

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