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- PDB-3evd: Crystal structure of GTP complex of yellow fever virus methyltran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3evd | ||||||
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Title | Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine | ||||||
![]() | RNA-directed RNA polymerase NS5 | ||||||
![]() | TRANSFERASE / yellow fever virus / NS5 methyltransferase / RNA cap binding / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Helicase / Hydrolase / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribonucleoprotein / RNA replication / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transmembrane / Viral nucleoprotein / Virion | ||||||
Function / homology | ![]() flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / 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 / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thompson, A.A. / Geiss, B.J. / Peersen, O.B. | ||||||
![]() | ![]() Title: Analysis of flavivirus NS5 methyltransferase cap binding. Authors: Geiss, B.J. / Thompson, A.A. / Andrews, A.J. / Sons, R.L. / Gari, H.H. / Keenan, S.M. / Peersen, O.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.1 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3evaC ![]() 3evbC ![]() 3evcC ![]() 3eveC ![]() 3evfC ![]() 3evgC ![]() 1l9kS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31290.809 Da / Num. of mol.: 1 Fragment: N-terminal domain 1-268 of RNA-directed RNA polymerase NS5: UNP residues 2507-2772 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P03314, mRNA (guanine-N7)-methyltransferase, RNA-directed RNA polymerase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SAH / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% v/v MPD, 0.1 M Tris-HCl pH 8.5, 2 mM DTT, 0.02% w/v Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45 Å / Num. obs: 100587 / % possible obs: 100 % / Redundancy: 10.85 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 10.15 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.427 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1L9K Resolution: 1.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing and refinement
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Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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