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Yorodumi- PDB-5cqe: 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1... -
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-Basic information
Entry | Database: PDB / ID: 5cqe | ||||||
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Title | 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) | ||||||
Components | Matrix protein 1 | ||||||
Keywords | VIRAL PROTEIN / matrix protein 1 / Influenza A virus (A/Puerto Rico/8/34(H1N1)) / CSGID / virulence / pathogenesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) Authors: Halavaty, A.S. / Minasov, G. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqe.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqe.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 5cqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqe ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqe | HTTPS FTP |
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-Related structure data
Related structure data | 1ea3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 0 - 157 / Label seq-ID: 24 - 181
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20952.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) Strain: A/Puerto Rico/8/1934 H1N1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P03485 |
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-Non-polymers , 5 types, 96 molecules
#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: ...Details: Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: Crystallization condition + sucrose (50%) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2015 |
Radiation | Monochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 22646 / Num. obs: 22646 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EA3 Resolution: 2.1→29.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 8.136 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.391 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→29.47 Å
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