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- PDB-5a1z: Cryo-EM structure of Dengue virus serotype 2 strain PVP94-07 comp... -

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Basic information

Entry
Database: PDB / ID: 5a1z
TitleCryo-EM structure of Dengue virus serotype 2 strain PVP94-07 complexed with human antibody 2D22 Fab at 37 degrees C
Components
  • ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
  • ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
  • ENVELOPE PROTEIN
  • MEMBRANE GLYCOPROTEIN
KeywordsVIRUS / DENGUE VIRUS / HUMAN ANTIBODY / CRYO-EM / NEUTRALIZATION
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 / viral life cycle / 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 / 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 / viral life cycle / 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 / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / 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 NS3 helicase, C-terminal helical 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Membrane glycoprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 2
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
Model type detailsCA ATOMS ONLY, CHAIN A, C, E, B, D, F, G, I, K, H, J, L AUTHOR G.FIBRIANSAH,K.D.IBARRA,T.S.NG,S.A. ...CA ATOMS ONLY, CHAIN A, C, E, B, D, F, G, I, K, H, J, L AUTHOR G.FIBRIANSAH,K.D.IBARRA,T.S.NG,S.A.SMITH,J.L.TAN,X.N.LIM,J.S.G.OOI,
AuthorsFibriansah, G. / Ibarra, K.D. / Ng, T.S. / Smith, S.A. / Tan, J.L. / Lim, X.N. / Ooi, J.S.G. / Kostyuchenko, V.A. / Wang, J. / de Silva, A.M. ...Fibriansah, G. / Ibarra, K.D. / Ng, T.S. / Smith, S.A. / Tan, J.L. / Lim, X.N. / Ooi, J.S.G. / Kostyuchenko, V.A. / Wang, J. / de Silva, A.M. / Harris, E. / Crowe Jr, J.E. / Lok, S.M.
CitationJournal: Science / Year: 2015
Title: DENGUE VIRUS. Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers.
Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / ...Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / James E Crowe / Shee-Mei Lok /
Abstract: There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. ...There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. We demonstrated that DENV serotype 2 (DENV2)-specific human monoclonal antibody (HMAb) 2D22 is therapeutic in a mouse model of antibody-enhanced severe dengue disease. We determined the cryo-electron microscopy (cryo-EM) structures of HMAb 2D22 complexed with two different DENV2 strains. HMAb 2D22 binds across viral envelope (E) proteins in the dimeric structure, which probably blocks the E protein reorganization required for virus fusion. HMAb 2D22 "locks" two-thirds of or all dimers on the virus surface, depending on the strain, but neutralizes these DENV2 strains with equal potency. The epitope defined by HMAb 2D22 is a potential target for vaccines and therapeutics.
History
DepositionMay 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Other
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_imaging / em_software
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 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
  • EMDB-2996
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  • Superimposition on EM map
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Assembly

Deposited unit
A: ENVELOPE PROTEIN
B: MEMBRANE GLYCOPROTEIN
C: ENVELOPE PROTEIN
D: MEMBRANE GLYCOPROTEIN
E: ENVELOPE PROTEIN
F: MEMBRANE GLYCOPROTEIN
G: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
H: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
I: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
J: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
K: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
L: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)264,79112
Polymers264,79112
Non-polymers00
Water00
1
A: ENVELOPE PROTEIN
B: MEMBRANE GLYCOPROTEIN
C: ENVELOPE PROTEIN
D: MEMBRANE GLYCOPROTEIN
E: ENVELOPE PROTEIN
F: MEMBRANE GLYCOPROTEIN
G: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
H: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
I: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
J: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
K: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
L: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
x 60


Theoretical massNumber of molelcules
Total (without water)15,887,485720
Polymers15,887,485720
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: ENVELOPE PROTEIN
B: MEMBRANE GLYCOPROTEIN
C: ENVELOPE PROTEIN
D: MEMBRANE GLYCOPROTEIN
E: ENVELOPE PROTEIN
F: MEMBRANE GLYCOPROTEIN
G: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
H: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
I: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
J: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
K: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
L: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
x 5


  • icosahedral pentamer
  • 1.32 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,323,95760
Polymers1,323,95760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: ENVELOPE PROTEIN
B: MEMBRANE GLYCOPROTEIN
C: ENVELOPE PROTEIN
D: MEMBRANE GLYCOPROTEIN
E: ENVELOPE PROTEIN
F: MEMBRANE GLYCOPROTEIN
G: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
H: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
I: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
J: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
K: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN
L: ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN
x 6


  • icosahedral 23 hexamer
  • 1.59 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,588,74972
Polymers1,588,74972
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 ENVELOPE PROTEIN / E PROTEIN / Coordinate model: Cα atoms only


Mass: 54258.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 2 / Strain: PVP94-07
Description: THE C6/36 CELLS WERE INFECTED WITH DENGUE VIRUS SEROTYPE 2 STRAIN PVP94/07
Cell line (production host): C6/36 / Production host: AEDES ALBOPICTUS (Asian tiger mosquito) / References: UniProt: G9FRP5, UniProt: E0WXJ2*PLUS
#2: Protein MEMBRANE GLYCOPROTEIN / M PROTEIN / Coordinate model: Cα atoms only


Mass: 8109.491 Da / Num. of mol.: 3 / Fragment: RESIDUES 92-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 2 / Strain: PVP94-07
Description: THE C6/36 CELLS WERE INFECTED WITH DENGUE VIRUS SEROTYPE 2 STRAIN PVP94/07
Cell line (production host): C6/36 / Production host: AEDES ALBOPICTUS (Asian tiger mosquito) / References: UniProt: V5TI05, UniProt: E0WXJ2*PLUS
#3: Antibody ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - HEAVY CHAIN / Coordinate model: Cα atoms only


Mass: 13805.458 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: 180 COPIES OF FAB 2D22 MOLECULE BIND TO VIRUS SURFACE
Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-CELLS
#4: Antibody ANTIGEN-BINDING FRAGMENT OF HUMAN ANTIBODY 2D22 - LIGHT CHAIN / Coordinate model: Cα atoms only


Mass: 12090.306 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: 180 COPIES OF FAB 2D22 MOLECULE BIND TO VIRUS SURFACE
Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-CELLS

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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: DENGUE VIRUS SEROTYPE 2 STRAIN PVP94-07 (A CLINICAL ISOLATE) COMPLEXED WITH FAB FRAGMENTS OF HUMAN ANTIBODY 2D22.
Type: COMPLEX
Details: THE COMPLEX WAS INCUBATED AT 37 DEGREES C FOR 30 MIN
Buffer solutionName: 10 MM TRIS-HCL PH 8.0, 120 MM NACL AND 1 MM EDTA / pH: 8 / Details: 10 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
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOTTED WITH FILTER PAPER FOR 2 SECONDS PRIOR TO SNAP FREEZING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 27, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm
Image recordingElectron dose: 18 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 177

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Processing

EM software
IDNameVersionCategory
1MDFFmodel fitting
2NAMDmodel fitting
3UCSF Chimeramodel fitting
4EMAN13D reconstruction
5EMAN23D reconstruction
6MPSA3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 6.9 Å / Num. of particles: 3435 / Actual pixel size: 1.69 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2996. (DEPOSITION ID: 13351).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: REAL-SPACE CORRELATION / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 3J27

3j27


Accession code: 3J27 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.9 Å
Refinement stepCycle: LAST / Highest resolution: 6.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 0 0 2394

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