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

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Basic information

Entry
Database: PDB / ID: 4uta
TitleCrystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
Components
  • (BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 ...) x 2
  • ENVELOPE GLYCOPROTEIN E
KeywordsIMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / VIRAL PROTEIN / MEMBRANE FUSION / CLASS 2 FUSION PROTEIN / DENGUE VIRUS / BROADLY NEUTRALIZING ANTIBODY
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / 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 / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
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 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily ...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 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 2
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / chem_comp ...atom_site / 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 / _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 EDE1 C8 HEAVY CHAIN
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,0158
Polymers200,2256
Non-polymers1,7902
Water1,18966
1
B: ENVELOPE GLYCOPROTEIN E
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1694
Polymers100,1133
Non-polymers1,0571
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-32.7 kcal/mol
Surface area44680 Å2
MethodPQS
2
A: ENVELOPE GLYCOPROTEIN E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8454
Polymers100,1133
Non-polymers7331
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-33 kcal/mol
Surface area45890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.657, 191.342, 203.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.003, -0.003), (-0.003, -0.153, 0.988), (0.003, 0.988, 0.153)37.091, 29.776, -25.274
2given(-0.998, -0.035, -0.045), (-0.039, -0.159, 0.987), (-0.042, 0.987, 0.157)36.148, 30.827, -23.476
3given(-0.998, -0.044, -0.055), (-0.048, -0.155, 0.987), (-0.052, 0.987, 0.152)36.291, 31.13, -22.956

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Components

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Antibody , 2 types, 4 molecules HILM

#2: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN


Mass: 28882.834 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
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 EDE1 C8 LIGHT CHAIN


Mass: 23998.699 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
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, 68 molecules AB

#1: Protein ENVELOPE GLYCOPROTEIN E / E PROTEIN


Mass: 47230.980 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: Q68Y26, UniProt: A0A0B4SHY9*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 1
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

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Details

Sequence detailsTHE SEQUENCE MATCHES TO GENBANK CODE KM087965. THE RESIDUES AFTER W391 DERIVE FROM THE VECTOR. THE ...THE SEQUENCE MATCHES TO 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

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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: 3.05 Å3/Da / Density % sol: 0.59 % / Description: NONE
Crystal growDetails: 100MM TRIS PH 8.5, 18% (W/V) PEG 8000, 200MM LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 45639 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 88.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.2 / % possible all: 97.6

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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 3KDM AND 3EYF

3kdm

3eyf


Resolution: 3→19.97 Å / Cor.coef. Fo:Fc: 0.9085 / Cor.coef. Fo:Fc free: 0.8763 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2306 5.07 %RANDOM
Rwork0.2128 ---
obs0.2145 45462 95.57 %-
Displacement parametersBiso mean: 88.63 Å2
Baniso -1Baniso -2Baniso -3
1-3.2844 Å20 Å20 Å2
2---16.861 Å20 Å2
3---13.5766 Å2
Refine analyzeLuzzati coordinate error obs: 0.454 Å
Refinement stepCycle: LAST / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12491 0 120 66 12677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112923HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2717559HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4409SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes281HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1850HARMONIC5
X-RAY DIFFRACTIONt_it12923HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion20.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1749SEMIHARMONIC5
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_contact14139SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2683 168 5 %
Rwork0.2435 3190 -
all0.2448 3358 -
obs--95.57 %

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