[English] 日本語
Yorodumi
- PDB-3j42: Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j42
TitleObstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody
Components
  • Envelope protein E
  • Ig heavy chain V region MOPC 21, Igh protein chimera
  • Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
  • PrM
KeywordsVIRUS/IMMUNE SYSTEM / Dengue / maturation / immature / antibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / immunoglobulin complex / 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 / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / immunoglobulin complex / 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 / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / adaptive immune response / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / immune response / host cell perinuclear region of cytoplasm / 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 / lipid binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane / plasma 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 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / 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 / Ig kappa chain V-V region MOPC 21 / : / Genome polyprotein / Igh protein / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dengue virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 21 Å
AuthorsWang, Z. / Pennington, J.G. / Jiang, W. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2013
Title: Obstruction of dengue virus maturation by Fab fragments of the 2H2 antibody.
Authors: Zhiqing Wang / Long Li / Janice G Pennington / Ju Sheng / Moh Lan Yap / Pavel Plevka / Geng Meng / Lei Sun / Wen Jiang / Michael G Rossmann /
Abstract: The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature ...The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature virus enters an acidic environment. During dengue virus maturation, spiky, immature, noninfectious virions change their structure to form smooth-surfaced particles in the slightly acidic environment of the trans-Golgi network, thereby allowing cellular furin to cleave the precursor-membrane proteins. The dengue virions become fully infectious when they release the cleaved precursor peptide upon reaching the neutral-pH environment of the extracellular space. Here we report on the cryo-electron microscopy structures of the immature virus complexed with the 2H2 antigen binding fragments (Fab) at different concentrations and under various pH conditions. At neutral pH and a high concentration of Fab molecules, three Fab molecules bind to three precursor-membrane proteins on each spike of the immature virus. However, at a low concentration of Fab molecules and pH 7.0, only two Fab molecules bind to each spike. Changing to a slightly acidic pH caused no detectable change of structure for the sample with a high Fab concentration but caused severe structural damage to the low-concentration sample. Therefore, the 2H2 Fab inhibits the maturation process of immature dengue virus when Fab molecules are present at a high concentration, because the three Fab molecules on each spike hold the precursor-membrane molecules together, thereby inhibiting the normal conformational change that occurs during maturation.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / struct_ref_seq_dif
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_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5674
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5674
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: PrM
E: PrM
F: PrM
G: Ig heavy chain V region MOPC 21, Igh protein chimera
H: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
I: Ig heavy chain V region MOPC 21, Igh protein chimera
J: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
K: Ig heavy chain V region MOPC 21, Igh protein chimera
L: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera


Theoretical massNumber of molelcules
Total (without water)299,14412
Polymers299,14412
Non-polymers00
Water00
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: PrM
E: PrM
F: PrM
G: Ig heavy chain V region MOPC 21, Igh protein chimera
H: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
I: Ig heavy chain V region MOPC 21, Igh protein chimera
J: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
K: Ig heavy chain V region MOPC 21, Igh protein chimera
L: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
x 60


Theoretical massNumber of molelcules
Total (without water)17,948,651720
Polymers17,948,651720
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 E
B: Envelope protein E
C: Envelope protein E
D: PrM
E: PrM
F: PrM
G: Ig heavy chain V region MOPC 21, Igh protein chimera
H: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
I: Ig heavy chain V region MOPC 21, Igh protein chimera
J: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
K: Ig heavy chain V region MOPC 21, Igh protein chimera
L: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
x 5


  • icosahedral pentamer
  • 1.5 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,495,72160
Polymers1,495,72160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: PrM
E: PrM
F: PrM
G: Ig heavy chain V region MOPC 21, Igh protein chimera
H: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
I: Ig heavy chain V region MOPC 21, Igh protein chimera
J: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
K: Ig heavy chain V region MOPC 21, Igh protein chimera
L: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
x 6


  • icosahedral 23 hexamer
  • 1.79 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,794,86572
Polymers1,794,86572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein Envelope protein E / Coordinate model: Cα atoms only


Mass: 43400.898 Da / Num. of mol.: 3 / Fragment: UNP residues 281-675 / Source method: isolated from a natural source / Source: (natural) Dengue virus 2 / References: UniProt: O11875
#2: Protein PrM / Coordinate model: Cα atoms only


Mass: 9261.531 Da / Num. of mol.: 3 / Fragment: UNP residues 1-81 / Source method: isolated from a natural source / Source: (natural) Dengue virus 2 / References: UniProt: Q3BCY5
#3: Antibody Ig heavy chain V region MOPC 21, Igh protein chimera / 2H2 heavy chain Fab


Mass: 23696.553 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh-1a, Igh / References: UniProt: P01783, UniProt: Q6PIP8
#4: Antibody Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera / 2H2 light chain Fab


Mass: 23355.746 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm16939 / References: UniProt: P01634, UniProt: Q7TS98
Has protein modificationY
Sequence details2H2 HEAVY CHAIN FAB IS A CHIMERA COMPRISING RESIDUES 17-119 OF UNP P01783 AND RESIDUES 120-230 OF ...2H2 HEAVY CHAIN FAB IS A CHIMERA COMPRISING RESIDUES 17-119 OF UNP P01783 AND RESIDUES 120-230 OF UNP Q6PIP8 CONNECTED BY A HIS-TYR LINKER. 2H2 LIGHT CHAIN FAB IS A CHIMERA COMPRISING RESIDUES 30-136 OF UNP P01634 AND RESIDUES 130-234 OF UNP Q7TS98.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus at pH 7
Type: VIRUS
Details: Three Fab fragments bind to three pr on each trimeric spike
Details of virusEmpty: NO / Enveloped: YES / Host category: INVERTEBRATE / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Aedes albopictus / Strain: C6-36
Buffer solutionName: 100 mM phosphate buffer / pH: 7 / Details: 100 mM phosphate buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil 200 mesh
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 100 K / Details: Plunged into liquid ethane (homemade plunger)

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Apr 7, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51040 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 100 K / Temperature (max): 105 K / Temperature (min): 80 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 49
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1EMfitmodel fitting
2EMAN13D reconstruction
3EMAN23D reconstruction
4jspr3D reconstruction
CTF correctionDetails: Film
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 21 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 378 / Nominal pixel size: 3.72 Å / Actual pixel size: 3.72 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13C6D

3c6d

13C6D1PDBexperimental model
24KVC

4kvc

14KVC2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms11226 0 0 0 11226

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more