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- PDB-4cct: Dengue 1 cryo-EM reconstruction -

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Basic information

Entry
Database: PDB / ID: 4cct
TitleDengue 1 cryo-EM reconstruction
Components
  • DENGUE VIRUS 1 E PROTEIN
  • DENGUE VIRUS 1 M PROTEIN
KeywordsVIRUS / FLAVIVIRUS
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 / viral capsid / double-stranded RNA binding / channel activity / 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 / 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 / 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
Biological speciesDENGUE VIRUS 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F
AuthorsKostyuchenko, V.A. / Zhang, Q. / Tan, J.L. / Ng, T.S. / Lok, S.M.
CitationJournal: J Virol / Year: 2013
Title: Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.
Authors: Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok /
Abstract: Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, ...Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.
History
DepositionOct 28, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionNov 6, 2013ID: 4AZX
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3May 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

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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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-2142
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  • Superimposition on EM map
  • EMDB-2142
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-2142
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 M PROTEIN
E: DENGUE VIRUS 1 M PROTEIN
F: DENGUE VIRUS 1 M PROTEIN


Theoretical massNumber of molelcules
Total (without water)185,8546
Polymers185,8546
Non-polymers00
Water00
1
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 M PROTEIN
E: DENGUE VIRUS 1 M PROTEIN
F: DENGUE VIRUS 1 M PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)11,151,220360
Polymers11,151,220360
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: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 M PROTEIN
E: DENGUE VIRUS 1 M PROTEIN
F: DENGUE VIRUS 1 M PROTEIN
x 5


  • icosahedral pentamer
  • 929 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)929,26830
Polymers929,26830
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 M PROTEIN
E: DENGUE VIRUS 1 M PROTEIN
F: DENGUE VIRUS 1 M PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.12 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,115,12236
Polymers1,115,12236
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 DENGUE VIRUS 1 E PROTEIN / Coordinate model: Cα atoms only


Mass: 53908.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS 1 / Strain: PVP159 (DEN1/SG/07K3640DK1/2008) / References: UniProt: G3F5K5
#2: Protein DENGUE VIRUS 1 M PROTEIN / Coordinate model: Cα atoms only


Mass: 8042.396 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS 1 / Strain: PVP159 (DEN1/SG/07K3640DK1/2008) / References: UniProt: G3F5K5
Sequence detailsLABORATORY STRAIN, HAS SEVERAL MUTATIONS COMPARED TO ITS PART OF WHOLE POLYPROTEIN DESCRIBED IN ...LABORATORY STRAIN, HAS SEVERAL MUTATIONS COMPARED TO ITS PART OF WHOLE POLYPROTEIN DESCRIBED IN AEM92304.1 SEQUENCED AS A PART OF POLYPROTEIN ENCODED BY THE VIRAL GENOME

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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: MATURE DENGUE VIRUS 1 / Type: VIRUS
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 16, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 75000 X / Nominal defocus max: 3441 nm / Nominal defocus min: 989 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 18 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 791
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategoryDetails
1UCSF Chimeramodel fitting
2EMAN13D reconstruction
3EMAN23D reconstructionGPU-ADAPTED
CTF correctionDetails: WIENER FILTER WEIGHTING EACH PARTICLE DURING 3D RECONSTRUCTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES IN MPSA / Resolution: 4.5 Å / Num. of particles: 6412 / Nominal pixel size: 1.2 Å / Actual pixel size: 1.2 Å
Details: FTER MODELING THE STRUCTURES WERE REGULARIZED USING MOLECULAR DYNAMICS WITH FLEXIBLE MOLECULAR DYNAMICS WITH FLEXIBLE FITTING PROTOCOL. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- ...Details: FTER MODELING THE STRUCTURES WERE REGULARIZED USING MOLECULAR DYNAMICS WITH FLEXIBLE MOLECULAR DYNAMICS WITH FLEXIBLE FITTING PROTOCOL. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2142.(DEPOSITION ID: 10897).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1TG8

1tg8


Accession code: 1TG8 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.5 Å
Refinement stepCycle: LAST / Highest resolution: 4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 0 0 1707

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