+Open data
-Basic information
Entry | Database: PDB / ID: 6z6b | ||||||
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Title | Structure of full-length La Crosse virus L protein (polymerase) | ||||||
Components |
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Keywords | VIRAL PROTEIN / RNA-dependent RNA polymerase | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding ...host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bunyavirus La Crosse La Crosse orthobunyavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.961 Å | ||||||
Authors | Cusack, S. / Gerlach, P. / Reguera, J. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Authors: Benoît Arragain / Grégory Effantin / Piotr Gerlach / Juan Reguera / Guy Schoehn / Stephen Cusack / Hélène Malet / Abstract: Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and ...Bunyavirales is an order of segmented negative-strand RNA viruses comprising several life-threatening pathogens against which no effective treatment is currently available. Replication and transcription of the RNA genome constitute essential processes performed by the virally encoded multi-domain RNA-dependent RNA polymerase. Here, we describe the complete high-resolution cryo-EM structure of La Crosse virus polymerase. It reveals the presence of key protruding C-terminal domains, notably the cap-binding domain, which undergoes large movements related to its role in transcription initiation, and a zinc-binding domain that displays a fold not previously observed. We capture the polymerase structure at pre-initiation and elongation states, uncovering the coordinated movement of the priming loop, mid-thumb ring linker and lid domain required for the establishment of a ten-base-pair template-product RNA duplex before strand separation into respective exit tunnels. These structural details and the observed dynamics of key functional elements will be instrumental for structure-based development of polymerase inhibitors. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z6b.cif.gz | 918.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z6b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/6z6b ftp://data.pdbj.org/pub/pdb/validation_reports/z6/6z6b | HTTPS FTP |
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-Related structure data
Related structure data | 6z6gC 6z8kC 5amrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: RNA chain | Mass: 3217.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: vRNA 5' end (1-10) / Source: (synth.) La Crosse orthobunyavirus #2: RNA chain | Mass: 5044.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: vRNA 3' end (1-16) / Source: (synth.) La Crosse orthobunyavirus #3: RNA chain | Mass: 2510.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: vRNA 5' end (9-16) / Source: (synth.) La Crosse orthobunyavirus #4: Protein | Mass: 266047.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag / Source: (gene. exp.) Bunyavirus La Crosse / Production host: Trichoplusia ni (cabbage looper) References: UniProt: A5HC98, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.42 Å3/Da / Density % sol: 77.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: LACV-L in complex with pre-annealed 3 prime (1-16) and 5 prime (9-16) vRNA was concentrated to 5 mg/ml. The 5 prime (1-10) vRNA end was later soaked into crystals in 1 to 2 molar ratio. ...Details: LACV-L in complex with pre-annealed 3 prime (1-16) and 5 prime (9-16) vRNA was concentrated to 5 mg/ml. The 5 prime (1-10) vRNA end was later soaked into crystals in 1 to 2 molar ratio. Mother liquor was 100 mM Tris pH 8.0, 100 mM NaCl, and 8% PEG 4000. Crystals were soaked in a stepwise manner with increasing concentration of the glycerol cryo-protectant, reaching 30% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 3.96→209.891 Å / Num. obs: 59211 / % possible obs: 60.8 % / Redundancy: 11.6 % / CC1/2: 0.995 / Rrim(I) all: 0.163 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.96→4.35 Å / Num. unique obs: 2961 / CC1/2: 0.47 / Rrim(I) all: 1.285 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AMR Resolution: 3.961→209.891 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.828 / SU B: 62.711 / SU ML: 0.824 / Cross valid method: FREE R-VALUE / ESU R Free: 1.092 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 189.756 Å2
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Refinement step | Cycle: LAST / Resolution: 3.961→209.891 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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