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- PDB-4ut6: Crystal structure of dengue 2 virus envelope glycoprotein in comp... -

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Basic information

Entry
Database: PDB / ID: 4ut6
TitleCrystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 B7
Components
  • (BROADLY NEUTRALIZING HUMAN ANTIBODY ...) x 2
  • ENVELOPE GLYCOPROTEIN E
KeywordsVIRAL PROTEIN / MEMBRANE FUSION / CLASS 2 FUSION PROTEIN / DENGUE ANTIBODY NEUTRALIZATION / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesDENGUE VIRUS 2
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Rey, F.A.
Citation
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. / Kikuti, C.M. / Sanchez, M.E.N. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Sanchez, M.E.N. / 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.
#1: Journal: Nat Immunol / Year: 2015
Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton /
Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.
History
DepositionJul 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN E
B: ENVELOPE GLYCOPROTEIN E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 B7
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 B7
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,42310
Polymers199,8666
Non-polymers2,5564
Water46826
1
A: ENVELOPE GLYCOPROTEIN E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 B7
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2115
Polymers99,9333
Non-polymers1,2782
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-23.4 kcal/mol
Surface area35740 Å2
MethodPQS
2
B: ENVELOPE GLYCOPROTEIN E
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 B7
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2115
Polymers99,9333
Non-polymers1,2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-22.1 kcal/mol
Surface area35790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.277, 58.980, 191.573
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.697, 0.003, -0.717), (0.003, -1, -0.001), (-0.717, -0.001, -0.697)170.37415, 153.76939, 403.86893
2given(0.694, -0.72), (-0.005, -1, -0.006), (-0.72, 0.008, -0.694)171.08249, 154.43083, 402.21948
3given(0.69, -0.004, -0.724), (-0.013, -1, -0.006), (-0.724, 0.014, -0.69)172.18765, 154.49973, 400.86954

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Components

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Antibody , 2 types, 4 molecules HILM

#2: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 B7


Mass: 30161.291 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, HEAVY CHAIN, RESIDUES 1-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SEE SECONDARY REFERENCE / Cell: B-LYMPHOCYTE / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)
#3: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2


Mass: 22955.410 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, LIGHT CHAIN, RESIDUES -1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SEE SECONDARY REFERENCE / Cell: B-LYMPHOCYTE / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly)

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Protein / Non-polymers , 2 types, 28 molecules AB

#1: Protein ENVELOPE GLYCOPROTEIN E / E PROTEIN


Mass: 46816.547 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 2 / Strain: FGA-02 / Plasmid: PMT/BIP/V5-HIS / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: A0A0B4SHY9*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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: isolated from a genetically manipulated source
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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Details

Sequence detailsGENBANK CODE KM087965 THE RESIDUES AFTER W391 DERIVE FROM THE VECTOR. THE RESIDUES ARE NUMBERED ...GENBANK CODE KM087965 THE RESIDUES AFTER W391 DERIVE FROM THE VECTOR. THE RESIDUES ARE NUMBERED FROM 1392. RESIDUES 1392 TO 1394 COMPLETE THE G STRAND OF ENVELOPE GLYCOPROTEIN DOMAIN III THE CONSTANT DOMAIN OF THE FAB IS DISORDER IN THE STRUCTURE THE CONSTANT DOMAIN OF THE FAB IS DISORDER IN THE STRUCTURE

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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: 2.84 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 100MM TRIS PH 8.5, 16% (W/V) PEG 400, 200MM MGCL2, CRYOPROTECTED IN 22%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 37500 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 79.17 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2
Reflection shellResolution: 3.2→3.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.6 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1OKE, 3KDM AND 3H0T

1oke

3kdm

3h0t


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.8768 / Cor.coef. Fo:Fc free: 0.8328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.401
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1984 5.34 %RANDOM
Rwork0.212 ---
obs0.214 37165 98.63 %-
Displacement parametersBiso mean: 92.81 Å2
Baniso -1Baniso -2Baniso -3
1--28.7491 Å20 Å212.7579 Å2
2--19.5693 Å20 Å2
3---9.1799 Å2
Refine analyzeLuzzati coordinate error obs: 0.696 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9673 0 170 26 9869
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810090HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1313686HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3512SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1450HARMONIC5
X-RAY DIFFRACTIONt_it10090HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion21.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1363SEMIHARMONIC5
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_contact10961SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.29 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2493 149 5.45 %
Rwork0.2254 2586 -
all0.2267 2735 -
obs--98.63 %
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)
10.6234-0.38450.9580.5269-0.85091.852-0.0051-0.02690.0333-0.309-0.0107-0.2526-0.07160.07470.01580.24730.041-0.0258-0.304-0.02860.0406-26.486458.8179256.3097
20.1925-0.13060.18280.5989-0.73451.82580.12220.02-0.0684-0.50860.0737-0.06340.065-0.0666-0.19590.3341-0.0006-0.1257-0.304-0.02560.0618-31.517794.3128244.3332
37.40590.0392-1.89831.3692-0.03570.8224-0.1422-0.5998-0.3567-0.0238-0.281-0.44010.39350.48230.42310.31980.1347-0.03910.00760.1675-0.3198-12.767285.1163211.0254
46.9431-0.7815-2.50312.50630.11882.6060.13630.57310.5047-0.2761-0.281-0.4368-0.123-0.23590.1447-0.27960.0544-0.12780.18170.1588-0.018910.37568.1966265.7046
53.690.69472.94052.76710.83234.04850.066-0.5478-0.49670.59980.3006-0.48230.58650.1717-0.3667-0.13880.0897-0.1725-0.02350.04220.015-4.388149.791297.9589
61.5528-0.95312.29784.82330.24256.5807-0.03560.59910.4234-0.58240.27140.3221-0.5239-0.4757-0.23580.32950.0678-0.0832-0.24510.0586-0.3295-46.2424103.496199.4082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|295 A|501 - A|567 }
2X-RAY DIFFRACTION2{ B|1 - B|295 B|501 - B|567 }
3X-RAY DIFFRACTION3{ H|2 - H|111 L|4 - L|106 }
4X-RAY DIFFRACTION4{ I|2 - I|111 M|4 - M|107 }
5X-RAY DIFFRACTION5{ A|296 - A|1394 }
6X-RAY DIFFRACTION6{ B|296 - B|1394 }

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