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Yorodumi- PDB-1uon: REOVIRUS POLYMERASE LAMBDA-3 LOCALIZED BY ELECTRON CRYOMICROSCOPY... -
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-Basic information
Entry | Database: PDB / ID: 1uon | |||||||||
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Title | REOVIRUS POLYMERASE LAMBDA-3 LOCALIZED BY ELECTRON CRYOMICROSCOPY OF VIRIONS AT 7.6-A RESOLUTION | |||||||||
Components |
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Keywords | POLYMERASE / REOVIRUS / CRYOEM / CORE PROTEIN | |||||||||
Function / homology | Function and homology information viral genome replication / viral nucleocapsid / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / RNA binding Similarity search - Function | |||||||||
Biological species | REOVIRUS synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Zhang, X. / Walker, S.B. / Chipman, P.R. / Nibert, M.L. / Baker, T.S. | |||||||||
Citation | Journal: Nat Struct Biol / Year: 2003 Title: Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 A. Authors: Xing Zhang / Stephen B Walker / Paul R Chipman / Max L Nibert / Timothy S Baker / Abstract: Reovirus is an icosahedral, double-stranded (ds) RNA virus that uses viral polymerases packaged within the viral core to transcribe its ten distinct plus-strand RNAs. To localize these polymerases, ...Reovirus is an icosahedral, double-stranded (ds) RNA virus that uses viral polymerases packaged within the viral core to transcribe its ten distinct plus-strand RNAs. To localize these polymerases, the structure of the reovirion was refined to a resolution of 7.6 A by cryo-electron microscopy (cryo-EM) and three-dimensional (3D) image reconstruction. X-ray crystal models of reovirus proteins, including polymerase lambda 3, were then fitted into the density map. Each copy of lambda 3 was found anchored to the inner surface of the icosahedral core shell, making major contacts with three molecules of shell protein lambda 1 and overlapping, but not centering on, a five-fold axis. The overlap explains why only one copy of lambda 3 is bound per vertex. lambda 3 is furthermore oriented with its transcript exit channel facing a small channel through the lambda 1 shell, suggesting how the nascent RNA is passed into the large external cavity of the pentameric capping enzyme complex formed by protein lambda 2. | |||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1uon.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uon.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uon_validation.pdf.gz | 592.5 KB | Display | wwPDB validaton report |
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Full document | 1uon_full_validation.pdf.gz | 630.7 KB | Display | |
Data in XML | 1uon_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1uon_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uon ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uon | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 142423.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) REOVIRUS / Strain: T3D / References: UniProt: P17378, UniProt: Q8V1A3*PLUS |
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-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 1681.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 2461.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 355 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: REOVIRUS POLYMERASE LAMBDA-3 / Type: COMPLEX |
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Buffer solution | Name: TRIS / pH: 7.5 / Details: TRIS |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Crystal grow | *PLUS Method: cryo electron microscopy / Details: cryo electron microscopy |
-Electron microscopy imaging
EM imaging | Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1
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Image recording |
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Image scans | Num. digital images: 54 |
-Processing
EM software | Name: PFT / Category: 3D reconstruction / Details: PFT2D | ||||||||||||
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CTF correction | Details: INDIVIDUAL PARTICLES, PHASE AND AMPLITUDE | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: SPHERICAL HARMONICS / Resolution: 7.6 Å / Num. of particles: 7939 / Nominal pixel size: 2.3 Å / Actual pixel size: 2.21 Å / Magnification calibration: CROSS-CORRELATION Details: STRUCTURE OF REOVIRUS CORE (REINISCH ET AL. 2000 NATURE 404:960-967) (PDB ENTRY 1EJ6). PROTEIN ATOMS 9986, NUCLEIC ACID ATOMS 281, HETEROGEN ATOMS 86, SOLVENT ATOMS 350. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: METHOD--SITUS (CHACON ET AL, 2002 J. MOL. BIOL. 317,375-394) WAS USED TO FIT THE X-RAY STRUCTURE OF REOVIRUS POLYMERASE (TAO ET AL. 2002 CELL 111, 733-745) (PDB CODE 1N35) INTO THE EM ...Details: METHOD--SITUS (CHACON ET AL, 2002 J. MOL. BIOL. 317,375-394) WAS USED TO FIT THE X-RAY STRUCTURE OF REOVIRUS POLYMERASE (TAO ET AL. 2002 CELL 111, 733-745) (PDB CODE 1N35) INTO THE EM DENSITY OF THE 7.6-A RESOLUTION MAP OF REOVIRUS VIRIONS. THE COORDINATES OF THE FITTED REOVIRUS POLYMERASE WERE ALIGNED TO THE X-RAY STRUCTURE OF REOVIRUS CORE (REINISCH ET AL. 2000 NATURE 404,960-967) (PDB ENTRY 1EJ6). ALL MATRICES FOR BUILDING AN ICOSAHEDRON CAN BE FOUND IN 1EJ6. | ||||||||||||
Atomic model building | PDB-ID: 1UON Accession code: 1UON / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 7.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.6 Å
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