+Open data
-Basic information
Entry | Database: PDB / ID: 4cct | |||||||||
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Title | Dengue 1 cryo-EM reconstruction | |||||||||
Components |
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Keywords | VIRUS / 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 / protein complex oligomerization / monoatomic ion channel activity / 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 / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | |||||||||
Biological species | DENGUE VIRUS 1 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F | |||||||||
Authors | Kostyuchenko, V.A. / Zhang, Q. / Tan, J.L. / Ng, T.S. / Lok, S.M. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4cct.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cct.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cct_validation.pdf.gz | 953.3 KB | Display | wwPDB validaton report |
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Full document | 4cct_full_validation.pdf.gz | 952.8 KB | Display | |
Data in XML | 4cct_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4cct_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4cct ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4cct | HTTPS FTP |
-Related structure data
Related structure data | 2142MC 2141C 4b03C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | 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 | 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 details | LABORATORY STRAIN, HAS SEVERAL MUTATIONS COMPARED TO ITS PART OF WHOLE POLYPROTEIN DESCRIBED IN ...LABORATORY | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MATURE DENGUE VIRUS 1 / Type: VIRUS |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Dec 16, 2011 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Temperature: 100 K |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 791 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: WIENER FILTER WEIGHTING EACH PARTICLE DURING 3D RECONSTRUCTION | ||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: OTHER / Space: REAL Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||||
Atomic model building | PDB-ID: 1TG8 Accession code: 1TG8 / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement | Highest resolution: 4.5 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.5 Å
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