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Yorodumi- EMDB-11079: Helical reconstruction of influenza A virus M1 in complex with nu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11079 | ||||||||||||
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Title | Helical reconstruction of influenza A virus M1 in complex with nucleic acid | ||||||||||||
Map data | symmetrised helical reconstruction map | ||||||||||||
Sample |
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Keywords | M1 / Matrix protein / Influenza virus / Assembly / ribonucleoprotein complex / VIRAL PROTEIN | ||||||||||||
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 (strain A/Puerto Rico/8/1934 H1N1) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Xiong X / Qu K / Briggs JAG | ||||||||||||
Funding support | United Kingdom, European Union, Germany, 3 items
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Citation | Journal: Nature / Year: 2020 Title: The native structure of the assembled matrix protein 1 of influenza A virus. Authors: Julia Peukes / Xiaoli Xiong / Simon Erlendsson / Kun Qu / William Wan / Leslie J Calder / Oliver Schraidt / Susann Kummer / Stefan M V Freund / Hans-Georg Kräusslich / John A G Briggs / Abstract: Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by ...Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by forming an endoskeleton beneath the virus membrane. The structure of full-length M1, and how it oligomerizes to mediate the assembly of virions, is unknown. Here we determine the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We find that the C-terminal domain of M1 is disordered in solution but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerizing M1 into linear strands that coat the interior surface of the membrane of the assembling virion. In the M1 polymer, five histidine residues-contributed by three different monomers of M1-form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore reveal mechanisms of influenza virus assembly and disassembly. #1: Journal: Biorxiv / Year: 2020 Title: The native structure of the full-length, assembled influenza A virus matrix protein, M1. Authors: Peukes J / Xiong X / Erlendsson S / Qu K / Wan W / Calder LJ / Schraidt O / Kummer S / Freund SMV / Krausslich HG / Briggs JAG | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11079.map.gz | 110.5 MB | EMDB map data format | |
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Header (meta data) | emd-11079-v30.xml emd-11079.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_11079.png | 312.2 KB | ||
Masks | emd_11079_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-11079.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11079 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11079 | HTTPS FTP |
-Validation report
Summary document | emd_11079_validation.pdf.gz | 190.9 KB | Display | EMDB validaton report |
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Full document | emd_11079_full_validation.pdf.gz | 344.1 KB | Display | |
Data in XML | emd_11079_validation.xml.gz | 504 B | Display | |
Data in CIF | emd_11079_validation.cif.gz | 373 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11079 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11079 | HTTPS FTP |
-Related structure data
Related structure data | 6z5lMC 6z5jC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11079.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | symmetrised helical reconstruction map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.128 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11079_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Helical reconstruction of influenza A virus M1 protein in complex...
Entire | Name: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid |
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Components |
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-Supramolecule #1: Helical reconstruction of influenza A virus M1 protein in complex...
Supramolecule | Name: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Influenza A M1 in complex with 6.4 Kb DNA plasmid |
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Source (natural) | Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) |
Molecular weight | Theoretical: 28 KDa |
-Macromolecule #1: Matrix protein 1
Macromolecule | Name: Matrix protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) |
Molecular weight | Theoretical: 28.97143 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNKMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT ...String: MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNKMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT TNPLIRHENR MVLASTTAKA MEQMAGSSEQ AAEAMEVASQ ARQMVQAMRT IGTHPSSSAG LKNDLLENLQ AY QKRMGVQ MQRFKLEHHH HHH UniProtKB: Matrix protein 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 10 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: sample was applied 3 times each with 30s adsorption time. | |||||||||
Details | M1 at 0.1 mg/ml plasmid DNA at 0.25 mg/ml |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2347 / Average electron dose: 47.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number classes used: 1 Applied symmetry - Helical parameters - Δz: 3.08413 Å Applied symmetry - Helical parameters - Δ&Phi: -11.1081 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 17984 |
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Segment selection | Number selected: 463152 / Software - Name: SPRING (ver. 0.86) Software - details: Used for selecting segments of similar diameters Details: Manual picking |
Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.08) |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 37.9 / Target criteria: correlation coefficient |
Output model | PDB-6z5l: |