[English] 日本語
Yorodumi- PDB-5fmq: Crystal structure of the mid, cap-binding, mid-link and 627 domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fmq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mid, cap-binding, mid-link and 627 domains from avian influenza A virus polymerase PB2 subunit bound to M7GTP H32 crystal form | ||||||
Components | INFLUENZA A PB2 SUBUNIT | ||||||
Keywords | VIRAL PROTEIN / INFLUENZA A PB2-C REGION CONTAINING MID / CAP-BINDING / MID- LINK / 627 AND NLS DOMAINS | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / 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 / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Thierry, E. / Pflug, A. / Hart, D. / Cusack, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fmq.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fmq.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fmq ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fmq | HTTPS FTP |
---|
-Related structure data
Related structure data | 5epiC 5fmlC 5fmmC 5fmzC 3kc6S 4cb4S 4wsbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) INFLUENZA A VIRUS / Strain: A/VIETNAM/1203/2004(H5N1) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: Q6DNN3 |
---|---|
#2: Chemical | ChemComp-MGT / |
Nonpolymer details | 7N-METHYL-8-HYDROGUANO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.2 % Description: MERGING R VALUE OF INTENSITIES, OF THE DATA IN THE HIGHEST RESOLUTION SHELL IS ACTUALLY 1.66 BUT MAXIMUM OF 1. 5 ALLOWED IN DEPOSITION FORM |
---|---|
Crystal grow | pH: 5.8 Details: 0.1 M TRI-SODIUM CITRATE PH 5.8 AND 1 M AMMONIUM DI-HYDROGEN PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / 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: 3.2→50 Å / Num. obs: 11351 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.39 / Net I/σ(I): 8.21 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 10.98 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.02 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4WSB 4CB4 3KC6 Resolution: 3.1→96.68 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.831 / SU B: 32.029 / SU ML: 0.507 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 69.763 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→96.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|