#1: Journal: Proc Natl Acad Sci U S A / Year: 2004 Title: The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Authors: George Rice / Liang Tang / Kenneth Stedman / Francisco Roberto / Josh Spuhler / Eric Gillitzer / John E Johnson / Trevor Douglas / Mark Young / Abstract: Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at ...Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at some of the highest temperatures and extremes of pH of all known organisms. Phylogenetic rRNA-encoding DNA analysis places many of the hyperthermophilic Archaea (species with an optimum growth > or = 80 degrees C) at the base of the universal tree of life, suggesting that thermophiles were among the first forms of life on earth. Very few viruses have been identified from Archaea as compared to Bacteria and Eukarya. We report here the structure of a hyperthermophilic virus isolated from an archaeal host found in hot springs in Yellowstone National Park. The sequence of the circular double-stranded DNA viral genome shows that it shares little similarity to other known genes in viruses or other organisms. By comparing the tertiary and quaternary structures of the coat protein of this virus with those of a bacterial and an animal virus, we find conformational relationships among all three, suggesting that some viruses may have a common ancestor that precedes the division into three domains of life >3 billion years ago.
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
THE ANNOTATION FOR THIS ENTRY IS PREDICTED FROM THECRYSTAL STRUCTURE. HOWEVER, THE AUTHORS OF THIS ENTRYARE CURRENTLY INVESIGATING THE QUATERNARY STATE OFTHIS MOLECULE BY EXPERIMENTAL METHODS.
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Components
#1: Protein
A197
Mass: 24317.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / Strain: ISOLATE YNPRC179 Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C) IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN IN YELLOWSTONE NATIONAL PARK Plasmid: PEXP14-STIVA197 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q6Q0L5
Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence details
C-TERMINAL 6XHIS TAG WAS ADDED DURING CLONING, SELENOMETHIONINES IN PLACE OF METHIONINES
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2 Å3/Da / Density % sol: 37 %
Crystal grow
Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP VAPOR DIFFUSION IN 0.1 M MES(PH 6.5), 1.4 M (NH4)2SO4, 10% 1,4-DIOXANE; THEN CRYOPROTECTED BY A QUICK SOAK IN MOTHER LIQUOR PLUS 25% GLUCOSE.
Resolution: 1.86→30 Å / Num. obs: 15646 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2
Reflection shell
Resolution: 1.86→1.93 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datareduction
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.86→28.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.369 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS MOTION DETERMINATION SERVER (PAINTER & MERRITT (2005) ACTA CRYST. D61, 465-471) WAS USED FOR SELECTION OF OPTIMAL TLS GROUPS USED IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS MOTION DETERMINATION SERVER (PAINTER & MERRITT (2005) ACTA CRYST. D61, 465-471) WAS USED FOR SELECTION OF OPTIMAL TLS GROUPS USED IN FINAL REFINEMENT. AMINO ACIDS 139 TO 147 WERE NOT MODELED DUE TO THE ABSENCE OF INTERPRETABLE ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.204
768
4.9 %
RANDOM
Rwork
0.171
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obs
0.172
14813
95.5 %
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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