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- PDB-2r6p: Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoE... -

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Basic information

Entry
Database: PDB / ID: 2r6p
TitleFit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus.
Components
  • Heavy chain of 1A1D-2
  • Light chain of 1A1D-2
  • Major envelope protein E
KeywordsVirus/Immune System / Fab / dengue / virus / neutralization / Virus-Immune System COMPLEX / icosahedral virus
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / 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
Flavivirus envelope glycoprotein E, stem/anchor domain / 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 envelope glycoprotein E, Stem/Anchor domain ...Flavivirus envelope glycoprotein E, stem/anchor domain / 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 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Igh protein
Similarity search - Component
Biological speciesDengue virus 2 Puerto Rico/PR159-S1/1969
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 24 Å
AuthorsLok, S.M. / Kostyuchenko, V.K. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Nat Struct Mol Biol / Year: 2008
Title: Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.
Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / ...Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / Michael S Diamond / Richard J Kuhn / Michael G Rossmann /
Abstract: The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding ...The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization of the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Data collection / Data processing / Structure summary
Category: audit_author / em_image_scans / em_software / Item: _audit_author.name / _em_software.name
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Heavy chain of 1A1D-2
E: Light chain of 1A1D-2
F: Heavy chain of 1A1D-2
G: Light chain of 1A1D-2


Theoretical massNumber of molelcules
Total (without water)221,9667
Polymers221,9667
Non-polymers00
Water0
1
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Heavy chain of 1A1D-2
E: Light chain of 1A1D-2
F: Heavy chain of 1A1D-2
G: Light chain of 1A1D-2
x 60


Theoretical massNumber of molelcules
Total (without water)13,317,956420
Polymers13,317,956420
Non-polymers00
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: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Heavy chain of 1A1D-2
E: Light chain of 1A1D-2
F: Heavy chain of 1A1D-2
G: Light chain of 1A1D-2
x 5


  • icosahedral pentamer
  • 1.11 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,109,83035
Polymers1,109,83035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Heavy chain of 1A1D-2
E: Light chain of 1A1D-2
F: Heavy chain of 1A1D-2
G: Light chain of 1A1D-2
x 6


  • icosahedral 23 hexamer
  • 1.33 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,331,79642
Polymers1,331,79642
Non-polymers00
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 Major envelope protein E / Coordinate model: Cα atoms only


Mass: 43403.984 Da / Num. of mol.: 3 / Fragment: E protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 Puerto Rico/PR159-S1/1969
Genus: Flavivirus / Species: Dengue virus / Strain: PR-159-S1 / Gene: E protein / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18356, UniProt: Q66394*PLUS
#2: Antibody Heavy chain of 1A1D-2 / Coordinate model: Cα atoms only


Mass: 23068.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balbc / Gene: immunoglobulin / Cell line (production host): hybridoma / References: UniProt: Q6PJB2*PLUS
#3: Antibody Light chain of 1A1D-2 / Coordinate model: Cα atoms only


Mass: 22808.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: balbc / Gene: immunoglobulin / Cell line (production host): hybridoma

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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

ComponentName: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
Type: VIRUS / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
Details of virusHost category: MOSQUITO / Type: VIRION
Natural hostOrganism: Aedes albopictus / Strain: C6/36 cells
Buffer solutionpH: 7.6
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Date: Mar 21, 2007 / Details: low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51040 X / Nominal defocus max: 3373 nm / Nominal defocus min: 2276 nm / Cs: 2 mm
Specimen holderTemperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 2.39 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2SPIDER3D reconstruction
3Xmipp3D reconstruction
CTF correctionDetails: phase flip
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 24 Å / Num. of particles: 2885 / Actual pixel size: 2.74 Å / Details: THE COORDINATES IN THIS ENTRY CONTAIN CA ONLY / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Using EMFIT
Details: METHOD--place coordinates manually and then optimise position using program REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1THD

1thd


Accession code: 1THD / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 0 0 2006

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