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- PDB-1h1k: THE BLUETONGUE VIRUS (BTV) CORE BINDS DSRNA -

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Basic information

Entry
Database: PDB / ID: 1h1k
TitleTHE BLUETONGUE VIRUS (BTV) CORE BINDS DSRNA
Components(RNA) x 6
KeywordsVIRUS/VIRAL PROTEIN/RNA / VIRUS / VIRAL PROTEIN / RNA / VIRUS-VIRAL PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBLUETONGUE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 10 Å
AuthorsDiprose, J.M. / Grimes, J.M. / Sutton, G.C. / Burroughs, J.N. / Meyer, A. / Maan, S. / Mertens, P.P.C. / Stuart, D.I.
Citation
Journal: J.Virol. / Year: 2002
Title: The Core of Bluetongue Virus Binds Double-Stranded RNA
Authors: Diprose, J.M. / Grimes, J.M. / Sutton, G.C. / Burroughs, J.N. / Meyer, A. / Maan, S. / Mertens, P.P.C. / Stuart, D.I.
#1: Journal: Nature / Year: 1998
Title: The Atomic Structure of the Bluetongue Virus Core
Authors: Grimes, J.M. / Burroughs, J.N. / Gouet, P. / Diprose, J.M. / Malby, R. / Zientras, S. / Mertens, P.P. / Stuart, D.I.
History
DepositionJul 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: RNA
J: RNA
K: RNA
L: RNA
M: RNA
N: RNA


Theoretical massNumber of molelcules
Total (without water)605,2386
Polymers605,2386
Non-polymers00
Water00
1
I: RNA
L: RNA


Theoretical massNumber of molelcules
Total (without water)261,6832
Polymers261,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
J: RNA
M: RNA


Theoretical massNumber of molelcules
Total (without water)175,2722
Polymers175,2722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
K: RNA
N: RNA


Theoretical massNumber of molelcules
Total (without water)168,2832
Polymers168,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)795.600, 821.800, 753.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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RNA chain , 6 types, 6 molecules IJKLMN

#1: RNA chain RNA


Mass: 135587.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)
#2: RNA chain RNA


Mass: 90815.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)
#3: RNA chain RNA


Mass: 87194.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)
#4: RNA chain RNA


Mass: 126095.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)
#5: RNA chain RNA


Mass: 84456.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)
#6: RNA chain RNA


Mass: 81088.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BLUETONGUE VIRUS / Strain: STEROTYPE 1 (SOUTH AFRICA)

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Details

Compound detailsTHIS ENTRY CORRESPONDS TO ONLY THE RNA MODEL WHICH WAS BUILT INTO THE BLUE TONGUE VIRUS STRUCTURE ...THIS ENTRY CORRESPONDS TO ONLY THE RNA MODEL WHICH WAS BUILT INTO THE BLUE TONGUE VIRUS STRUCTURE DATA. IN ORDER TO VIEW THE WHOLE VIRUS IN CONJUNCTION WITH THE NUCLEIC ACID TEMPLATE, THIS ENTRY MUST BE SEEN TOGETHER WITH PDB ENTRY 2BTV, WHICH ALSO CONTAINS THE SYMMETRY TRANSFORMATIONS NECESSARY TO BUILD THE WHOLE CAPSID.
Sequence detailsTHIS SUBMISSION IS AN RNA MODEL THAT HAS BEEN RIGID BODY FITTED INTO A 10A DIFFERENCE FOURIER ...THIS SUBMISSION IS AN RNA MODEL THAT HAS BEEN RIGID BODY FITTED INTO A 10A DIFFERENCE FOURIER ELECTRON DENSITY MAP BETWEEN NATIVE BLUETONGUE CORE DATA AND THE MODEL FOR THE CORE PARTICLE. THERE IS NO RELEVANCE IN THE SEQUENCE OF THE BASES IN THE RNA MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1045

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Sample preparation

CrystalDescription: OVER 1000 CRYSTALS EXAMINED. DATA WERE COLLECTED DURING 1995-1997. WAVELENGTHS BETWEEN 0.87 - 1.00.
Crystal growpH: 8
Details: 15% AMMONIUM SULPHATE, 25% ETHYLENE GLYCOL, 0.1M TRIS/HCL BUFFER PH 8.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop / Details: Diprose, J.M., (2001) EMBO J., 20, 7229.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %satammonium sulfate1reservoir
225 %ethylene glycol1reservoir
30.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 3524397 / % possible obs: 54 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 2.9
Reflection shellResolution: 3.5→4 Å / Redundancy: 1.06 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 0.72 / % possible all: 7.8
Reflection
*PLUS
Highest resolution: 10 Å / Lowest resolution: 105 Å / Num. obs: 251202 / % possible obs: 94.7 % / Num. measured all: 490727 / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 10 Å
Details: THE MODEL WAS BUILT INTO A 10A DIFFERENCE FOURIER ELECTRON DENSITY MAP CALCULATED BETWEEN NATIVE BLUETONGUE CORE DATA AND THE MODEL FOR THE CORE PARTICLE. CNS WAS USED TO RIGID BODY REFINE ...Details: THE MODEL WAS BUILT INTO A 10A DIFFERENCE FOURIER ELECTRON DENSITY MAP CALCULATED BETWEEN NATIVE BLUETONGUE CORE DATA AND THE MODEL FOR THE CORE PARTICLE. CNS WAS USED TO RIGID BODY REFINE THE MODEL AGAINST THE STRUCTURE FACTOR AMPLITUDES CALCULATED FROM THE DIFFERENCE MAP USING BASE PAIRS AS RIGID BODIES.
Refinement stepCycle: LAST / Highest resolution: 10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 40008 0 0 40008

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