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- PDB-6idi: Cryo-EM structure of Immature Dengue virus serotype 3 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6idi
TitleCryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0.
Components
  • Envelope protein
  • Fab 1H10 heavy chain (V-region)
  • Fab 1H10 light chain (V-region)
  • Premembrane protein
KeywordsVIRUS / immature dengue virus / human 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 / double-stranded RNA binding / channel activity / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...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 / double-stranded RNA binding / channel activity / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / 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 central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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 / 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
Biological speciesDengue virus 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsWirawan, M. / Fibriansah, G. / Ng, T.S. / Zhang, Q. / Kostyuchenko, V.A. / Shi, J. / Lok, S.M.
Funding support Singapore, United States, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
Ministry of Education (MoE, Singapore)MOE2012-T3-008 Singapore
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI057157 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI103038 United States
CitationJournal: Structure / Year: 2019
Title: Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody.
Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / ...Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / Ganesh Anand / James E Crowe / Peter J Bond / Shee-Mei Lok /
Abstract: Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti- ...Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unknown how anti-prM antibody-coated particles can undergo membrane fusion since the prM caps the envelope (E) protein fusion loop. Here, we determined cryoelectron microscopy (cryo-EM) maps of the immDENV:anti-prM complex at different pH values, mimicking the extracellular (pH 8.0) or endosomal (pH 5.0) environments. At pH 5.0, there are two structural classes with fewer antibodies bound than at pH 8.0. These classes may represent different maturation states. Molecular simulations, together with the measured high-affinity pr:antibody interaction (versus the weak pr:E interaction) and also the low pH cryo-EM structures, suggest how antibody:pr complex can dislodge from the E protein at low pH. This exposes the E protein fusion loop enhancing virus interaction with endosomes.
History
DepositionSep 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 2.0Jun 3, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / em_entity_assembly ...atom_site / em_entity_assembly / em_entity_assembly_naturalsource / em_software / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_poly_seq_scheme / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues / struct_ref_seq
Item: _em_entity_assembly.name / _em_entity_assembly_naturalsource.strain ..._em_entity_assembly.name / _em_entity_assembly_naturalsource.strain / _em_software.category / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_audit_support.funding_organization / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Mar 27, 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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Assembly

Deposited unit
A: Envelope protein
B: Envelope protein
C: Envelope protein
D: Premembrane protein
E: Premembrane protein
F: Premembrane protein
H: Fab 1H10 heavy chain (V-region)
I: Fab 1H10 heavy chain (V-region)
J: Fab 1H10 light chain (V-region)
L: Fab 1H10 light chain (V-region)
M: Fab 1H10 heavy chain (V-region)
N: Fab 1H10 light chain (V-region)


Theoretical massNumber of molelcules
Total (without water)299,46212
Polymers299,46212
Non-polymers00
Water00
1
A: Envelope protein
B: Envelope protein
C: Envelope protein
D: Premembrane protein
E: Premembrane protein
F: Premembrane protein
H: Fab 1H10 heavy chain (V-region)
I: Fab 1H10 heavy chain (V-region)
J: Fab 1H10 light chain (V-region)
L: Fab 1H10 light chain (V-region)
M: Fab 1H10 heavy chain (V-region)
N: Fab 1H10 light chain (V-region)
x 60


Theoretical massNumber of molelcules
Total (without water)17,967,691720
Polymers17,967,691720
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: Envelope protein
C: Envelope protein
D: Premembrane protein
E: Premembrane protein
F: Premembrane protein
H: Fab 1H10 heavy chain (V-region)
I: Fab 1H10 heavy chain (V-region)
J: Fab 1H10 light chain (V-region)
L: Fab 1H10 light chain (V-region)
M: Fab 1H10 heavy chain (V-region)
N: Fab 1H10 light chain (V-region)
x 5


  • icosahedral pentamer
  • 1.5 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,497,30860
Polymers1,497,30860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope protein
B: Envelope protein
C: Envelope protein
D: Premembrane protein
E: Premembrane protein
F: Premembrane protein
H: Fab 1H10 heavy chain (V-region)
I: Fab 1H10 heavy chain (V-region)
J: Fab 1H10 light chain (V-region)
L: Fab 1H10 light chain (V-region)
M: Fab 1H10 heavy chain (V-region)
N: Fab 1H10 light chain (V-region)
x 6


  • icosahedral 23 hexamer
  • 1.8 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,796,76972
Polymers1,796,76972
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 / Coordinate model: Cα atoms only


Mass: 53682.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: isolated from dengue patient / Source: (gene. exp.) Dengue virus 3 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A9LID6
#2: Protein Premembrane protein / Coordinate model: Cα atoms only


Mass: 18686.615 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: isolated from dengue patient / Source: (gene. exp.) Dengue virus 3 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A9LID6
#3: Antibody Fab 1H10 heavy chain (V-region) / Coordinate model: Cα atoms only


Mass: 15319.042 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
#4: Antibody Fab 1H10 light chain (V-region) / Coordinate model: Cα atoms only


Mass: 12132.362 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))

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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
IDNameTypeDetailsEntity IDParent-IDSource
1Dengue virus 3 in complex with human antibodyCOMPLEXThe virus was isolated from dengue patient. The immature dengue 3 virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody 1H10 was generated from EBV-immortalized PBMC that was obtained from dengue patient.all0RECOMBINANT
2envelope proteinVIRUS#11RECOMBINANT
3Premembrane proteinVIRUS#21RECOMBINANT
4Fab 1H10COMPLEX#3-#41RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Dengue virus 311069
23Dengue virus 311069
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Aedes albopictus (Asian tiger mosquito)7160
23Aedes albopictus (Asian tiger mosquito)7160
34Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))10377
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
12NOYESSTRAINVIRION
23NOYESSTRAINVIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 18 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9MPSAinitial Euler assignment
10MPSAfinal Euler assignment
12MPSA3D reconstruction
13MDFFmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 9193
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2886 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4B03

4b03


Accession code: 4B03 / Source name: PDB / Type: experimental model

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