Journal: J Mol Biol / Year: 2013 Title: Surface for catalysis by poliovirus RNA-dependent RNA polymerase. Authors: Jing Wang / John M Lyle / Esther Bullitt / Abstract: The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of ...The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of subunits that propagate along a strong protein-protein interaction called interface-I, as was observed in the crystal structure of wild-type poliovirus polymerase. These "filaments" recur with slight modifications in planar sheets and, with additional modifications that accommodate curvature, in helical tubes of the polymerase, by packing filaments together via a second set of interactions. Periodic variations of subunit orientations within 3Dpol tubes give rise to "ghost reflections" in diffraction patterns computed from electron cryomicrographs of helical arrays. The ghost reflections reveal that polymerase tubes are formed by bundles of four to five interface-I filaments, which are then connected to the next bundle of filaments with a perturbation of interface interactions between bundles. While enzymatically inactive polymerase is also capable of oligomerization, much thinner tubes that lack interface-I interactions between adjacent subunits are formed, suggesting that long-range allostery produces conformational changes that extend from the active site to the protein-protein interface. Macromolecular assemblies of poliovirus polymerase show repeated use of flexible interface interactions for polymerase lattice formation, suggesting that adaptability of polymerase-polymerase interactions facilitates RNA replication. In addition, the presence of a positively charged groove identified in polymerase arrays may help position and stabilize the RNA template during replication.
History
Deposition
Dec 27, 2012
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Header (metadata) release
Jan 16, 2013
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Map release
Feb 12, 2014
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Update
Apr 23, 2014
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Current status
Apr 23, 2014
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5560.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Helical reconstruction of a tube of poliovirus polymerase, including ghost reflections
Voxel size
X=Y=Z: 3.4 Å
Density
Contour Level
By AUTHOR: 15.5 / Movie #1: 15.5
Minimum - Maximum
-34.0 - 62.0
Average (Standard dev.)
1.82832026 (±11.531558990000001)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
159
159
148
Spacing
159
159
148
Cell
A: 540.60004 Å / B: 540.60004 Å / C: 503.2 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
3.4
3.4
3.4
M x/y/z
159
159
148
origin x/y/z
0.000
0.000
0.000
length x/y/z
540.600
540.600
503.200
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-50
29
166
NX/NY/NZ
106
122
134
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
159
159
148
D min/max/mean
-34.000
62.000
1.828
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Supplemental data
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Sample components
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Entire : Oligomer of poliovirus polymerase; helical structure with ghost r...
Entire
Name: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
Components
Sample: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
Protein or peptide: poliovirus polymerase
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Supramolecule #1000: Oligomer of poliovirus polymerase; helical structure with ghost r...
Supramolecule
Name: Oligomer of poliovirus polymerase; helical structure with ghost reflections included type: sample / ID: 1000 / Oligomeric state: oligomer of 331 components / Number unique components: 1
Molecular weight
Theoretical: 17.4 MDa / Method: 52.5 kD monomer
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Macromolecule #1: poliovirus polymerase
Macromolecule
Name: poliovirus polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: 3Dpol Details: polymerase was oligomerized by incubation at 30C followed by incubation at 4C. Number of copies: 331 / Oligomeric state: oligomer / Recombinant expression: Yes
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