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- PDB-8jn1: Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 ... -

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Basic information

Entry
Database: PDB / ID: 8jn1
TitleCryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR)
Components
  • (Human antibody DENV-115 ...) x 2
  • Envelope protein (Fragment)
  • Polyprotein
KeywordsVIRUS / dengue virus / human antibody / dengue-antibody structure
Function / homology
Function and homology information


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 / virion membrane / extracellular region / membrane
Similarity search - Function
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 ...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 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFibriansah, G. / Ng, T.S. / Tan, A.W.K. / Shi, J. / Lok, S.M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
CitationJournal: To Be Published
Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants
Authors: Fibriansah, G. / Ng, T.S. / Lim, X.N. / Shebanova, A. / Ng, L.C. / Tan, S.L. / Tan, A.W.K. / Shi, J. / Crowe, J.E. / Lok, S.M.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope protein (Fragment)
B: Polyprotein
C: Envelope protein (Fragment)
D: Polyprotein
E: Envelope protein (Fragment)
F: Polyprotein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,26714
Polymers211,3978
Non-polymers2,8716
Water00
1
A: Envelope protein (Fragment)
B: Polyprotein
C: Envelope protein (Fragment)
D: Polyprotein
E: Envelope protein (Fragment)
F: Polyprotein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain
hetero molecules

A: Envelope protein (Fragment)
B: Polyprotein
C: Envelope protein (Fragment)
D: Polyprotein
E: Envelope protein (Fragment)
F: Polyprotein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,53528
Polymers422,79316
Non-polymers5,74112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Envelope protein (Fragment)


Mass: 53731.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A173H1Z3
#2: Protein Polyprotein


Mass: 8365.854 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Gene: PrM/M, E / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A330J7Q8

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Antibody , 2 types, 2 molecules HL

#3: Antibody Human antibody DENV-115 heavy chain


Mass: 13607.289 Da / Num. of mol.: 1
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 DENV-115 light chain


Mass: 11496.620 Da / Num. of mol.: 1
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)

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Sugars , 2 types, 6 molecules

#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

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 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg CCOMPLEX#1-#40MULTIPLE SOURCES
2Dengue virus serotype 3 strain EHIE46200Y19COMPLEX#1-#21RECOMBINANT
3Human antibody DENV-115 IgG (heavy and light chain)COMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
32Aedes albopictus (Asian tiger mosquito)7160
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NOYESSTRAINVIRION
22
33
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 DENV-115 IgG 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.
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: 4600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 22.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181866 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13J6S

3j6s

13J6S1PDBexperimental model
25IFA

5ifa

15IFA2PDBexperimental model
36QB6

6qb6

16QB63PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00430572
ELECTRON MICROSCOPYf_angle_d0.58841418
ELECTRON MICROSCOPYf_dihedral_angle_d5.0014236
ELECTRON MICROSCOPYf_chiral_restr0.0444848
ELECTRON MICROSCOPYf_plane_restr0.0035162

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