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- PDB-5fmm: crystal structure of the mid, cap-binding, mid-link and 627 domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fmm | ||||||
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Title | crystal structure of the mid, cap-binding, mid-link and 627 domains from avian influenza a virus polymerase PB2 subunit bound to M7GTP | ||||||
![]() | INFLUENZA A PB2 SUBUNIT | ||||||
![]() | VIRAL PROTEIN / INFLUENZA A PB2-C REGION CONTAINING MID / CAP-BINDING / MID-LINK / 627 AND NLS DOMAINS | ||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thierry, E. / Pflug, A. / Hart, D. / Cusack, S. | ||||||
![]() | ![]() Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains. Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 77.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 887.9 KB | Display | ![]() |
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Full document | ![]() | 897.5 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5epiC ![]() 5fmlC ![]() 5fmqC ![]() 5fmzC ![]() 3kc6S ![]() 4cb4S ![]() 4wsbS 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: 54739.852 Da / Num. of mol.: 1 / Fragment: PB2-C, RESIDUES 247-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MGT / |
#3: Chemical | ChemComp-FLC / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | CITRATE ANION (FLC): FROM BUFFER 7N-METHYL-8-HYDROGUANO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.2 % / Description: NONE |
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Crystal grow | pH: 5 Details: 0.1 M TRI-SODIUM CITRATE PH 5 10 % POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 26542 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.04 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 4WSB, 4CB4, 3KC6 Resolution: 2.4→84.24 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.261 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→84.24 Å
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Refine LS restraints |
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