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- PDB-8y3h: Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 N1... -

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Basic information

Entry
Database: PDB / ID: 8y3h
TitleCryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 N153Q mutant in complex with human antibody 2D22 Fab at 37 deg C
Components
  • Envelope protein
  • Human antibody 2D22 Fab heavy chain
  • Human antibody 2D22 Fab light chain
  • Membrane polyprotein
KeywordsVIRUS/IMMUNE SYSTEM / dengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane ...viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / extracellular region / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / 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 capsid protein C superfamily / 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 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
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesdengue virus type 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFibriansah, G. / Ng, T.S. / Lim, X.N. / Tan, A.W.K. / Shi, J. / Lok, S.M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other governmentMOH-OFIRG18may-0007 Singapore
CitationJournal: To Be Published
Title: Role of N-glycosylation at asparagine 153 of dengue envelope protein in immune response
Authors: Fibriansah, G. / Ng, T.S. / Lim, X.N. / Tan, A.W.K. / Shi, J. / Crowe, J.E. / Lok, S.M.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
B: Membrane polyprotein
C: Envelope protein
D: Membrane polyprotein
E: Envelope protein
F: Membrane polyprotein
G: Human antibody 2D22 Fab heavy chain
H: Human antibody 2D22 Fab light chain
I: Human antibody 2D22 Fab heavy chain
J: Human antibody 2D22 Fab light chain
K: Human antibody 2D22 Fab heavy chain
L: Human antibody 2D22 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,40715
Polymers265,74412
Non-polymers6643
Water00
1
A: Envelope protein
B: Membrane polyprotein
C: Envelope protein
D: Membrane polyprotein
E: Envelope protein
F: Membrane polyprotein
G: Human antibody 2D22 Fab heavy chain
H: Human antibody 2D22 Fab light chain
I: Human antibody 2D22 Fab heavy chain
J: Human antibody 2D22 Fab light chain
K: Human antibody 2D22 Fab heavy chain
L: Human antibody 2D22 Fab light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)15,984,435900
Polymers15,944,618720
Non-polymers39,817180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Envelope protein
B: Membrane polyprotein
C: Envelope protein
D: Membrane polyprotein
E: Envelope protein
F: Membrane polyprotein
G: Human antibody 2D22 Fab heavy chain
H: Human antibody 2D22 Fab light chain
I: Human antibody 2D22 Fab heavy chain
J: Human antibody 2D22 Fab light chain
K: Human antibody 2D22 Fab heavy chain
L: Human antibody 2D22 Fab light chain
hetero molecules
x 5


  • icosahedral pentamer
  • 1.33 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,332,03675
Polymers1,328,71860
Non-polymers3,31815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope protein
B: Membrane polyprotein
C: Envelope protein
D: Membrane polyprotein
E: Envelope protein
F: Membrane polyprotein
G: Human antibody 2D22 Fab heavy chain
H: Human antibody 2D22 Fab light chain
I: Human antibody 2D22 Fab heavy chain
J: Human antibody 2D22 Fab light chain
K: Human antibody 2D22 Fab heavy chain
L: Human antibody 2D22 Fab light chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.6 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,598,44490
Polymers1,594,46272
Non-polymers3,98218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Envelope protein / Genome polyprotein


Mass: 54300.633 Da / Num. of mol.: 3 / Mutation: N153Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 2 / Strain: D2Y98P / Gene: E / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A678XB23
#2: Protein Membrane polyprotein / Genome polyprotein


Mass: 8384.814 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 2 / Strain: D2Y98P / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A4GVG9
#3: Antibody Human antibody 2D22 Fab heavy chain


Mass: 13805.458 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): EXPI293F / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
#4: Antibody Human antibody 2D22 Fab light chain


Mass: 12090.306 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): EXPI293F / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
#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.: 3 / 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
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Dengue virus serotype 2 strain Y98P-PP1 N153Q mutant in complex with human antibody 2D22 Fab at 37 deg CCOMPLEX#1-#40RECOMBINANT
2Dengue serotype 2 strain D2Y98P-PP1 N153Q mutantCOMPLEX#1-#21RECOMBINANT
3Human antibody 2D22 Fab (heavy and light chains)COMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
42
53
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22dengue virus type 211060
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Aedes albopictus (Asian tiger mosquito)7160
33Homo sapiens (human)9606EXPI293F
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The purified virus was mixed with human antibody 2D22 Fab at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min, and then at 37 deg C for 30 min.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 23.22 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149073 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 4UIF

4uif


Accession code: 4UIF / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318813
ELECTRON MICROSCOPYf_angle_d0.44625488
ELECTRON MICROSCOPYf_dihedral_angle_d4.7572600
ELECTRON MICROSCOPYf_chiral_restr0.0412883
ELECTRON MICROSCOPYf_plane_restr0.0033225

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