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- PDB-1khv: Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-depende... -

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Basic information

Entry
Database: PDB / ID: 1khv
TitleCrystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Lu3+
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
Luciferase; domain 5 / DNA/RNA polymerases / Helix Hairpins - #320 / : / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A ...Luciferase; domain 5 / DNA/RNA polymerases / Helix Hairpins - #320 / : / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helix Hairpins / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Helix non-globular / Picornavirus/Calicivirus coat protein / Special / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Genome polyprotein
Similarity search - Component
Biological speciesRabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsNg, K.K. / Cherney, M.M. / Vazquez, A.L. / Machin, A. / Alonso, J.M. / Parra, F. / James, M.N.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase.
Authors: Ng, K.K. / Cherney, M.M. / Vazquez, A.L. / Machin, A. / Alonso, J.M. / Parra, F. / James, M.N.
History
DepositionDec 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0134
Polymers115,6632
Non-polymers3502
Water2,900161
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0062
Polymers57,8311
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0062
Polymers57,8311
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.300, 119.100, 158.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RNA-dependent RNA polymerase


Mass: 57831.375 Da / Num. of mol.: 2 / Fragment: (RESIDUES 1252-1767)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus / Genus: Lagovirus / Plasmid: pGEX-3D / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P27410, RNA-directed RNA polymerase
#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Lu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, potassium thiocyanate, L-proline, glycerol, hexanediol, CHAPS, lutetium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
210-12 %PEG80001reservoir
30.1 MTris-Cl1reservoirpH7.5
40.2 Msodium thiocyanate1reservoir
50.1 ML-proline1reservoir
615 %(w/v)glycerol1reservoir
77 %(v/v)1,6-hexanediol1reservoir
80.1 %(w/v)CHAPS1reservoir
95 mM1reservoirLuCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 1999
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 42943 / Num. obs: 42943 / % possible obs: 91.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5587 / Rsym value: 0.254 / % possible all: 82.4
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 125565
Reflection shell
*PLUS
Lowest resolution: 2.6 Å / % possible obs: 82.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→34.5 Å / Cor.coef. Fo:Fc: 0.928 / SU ML: 189.774 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.498 / ESU R Free: 0.294 / Stereochemistry target values: Engh & Huber
Details: Grouped TLS refinement was used, with individual domains refined as a single group.
RfactorNum. reflection% reflectionSelection details
Rfree0.26535 1306 3.1 %RANDOM
Rwork0.21676 ---
all0.22 42943 --
obs0.21819 41361 88 %-
Displacement parametersBiso mean: 30.167 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2---1.66 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7776 0 2 161 7939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9610761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2893987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.868151445
X-RAY DIFFRACTIONr_chiral_restr0.0920.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.34023
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5585
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.351
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.50524937
X-RAY DIFFRACTIONr_mcangle_it2.6422.57970
X-RAY DIFFRACTIONr_scbond_it3.9163.53010
X-RAY DIFFRACTIONr_scangle_it5.6984.52791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 85 -
Rwork0.257 2615 -
obs-2615 76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5940.1991-1.30751.8059-0.1610.6694-0.25821.06190.6007-0.13650.18290.2340.2128-0.29860.07530.1452-0.0314-0.06460.41750.28090.4169.779681.93251.6536
21.9786-0.78950.81583.0114-0.87722.0381-0.0987-0.09490.3670.19780.17290.0708-0.2283-0.2701-0.07420.0661-0.02260.01950.14660.05550.123311.197469.003220.6918
33.82620.23260.33912.49420.21092.0881-0.04860.4393-0.1003-0.55340.0761-0.24540.24910.0403-0.02750.2206-0.0701-0.00770.07680.01980.040721.46250.91747.8441
42.29361.8098-1.22615.9602-2.41851.7481-0.0210.30580.1501-0.0626-0.0292-0.54170.1438-0.11250.05010.0384-0.01780.04590.26460.19150.414436.684175.49611.5827
57.658110.67420.151915.05510.45740.9728-0.53510.45340.4337-0.74380.63730.75360.0061-0.2016-0.10220.2733-0.009-0.08840.26830.07470.064132.723777.588138.9817
62.53131.13780.39113.8273-0.2562.21670.1096-0.3174-0.29960.6021-0.0138-0.31950.1299-0.0396-0.09590.2614-0.008-0.08170.19170.01230.050536.924166.81358.4039
75.47812.6409-0.48235.54731.51212.53840.16440.016-1.39430.24010.2909-1.94540.39020.562-0.45540.24750.1853-0.18240.2996-0.18710.910560.383862.731652.851
82.9609-0.08360.96465.17920.06281.9256-0.20280.0663-0.2399-0.05710.3996-0.5017-0.00290.1723-0.19690.12310.02440.03760.1172-0.10840.13154.396791.962749.0953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 655 - 65
2X-RAY DIFFRACTION2AA66 - 21566 - 215
3X-RAY DIFFRACTION2AA252 - 312252 - 312
4X-RAY DIFFRACTION3AA216 - 251216 - 251
5X-RAY DIFFRACTION3AA313 - 400313 - 400
6X-RAY DIFFRACTION4AA401 - 501401 - 501
7X-RAY DIFFRACTION5BB5 - 655 - 65
8X-RAY DIFFRACTION6BB66 - 21566 - 215
9X-RAY DIFFRACTION6BB252 - 312252 - 312
10X-RAY DIFFRACTION7BB216 - 251216 - 251
11X-RAY DIFFRACTION7BB313 - 400313 - 400
12X-RAY DIFFRACTION8BB401 - 501401 - 501
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.19
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor Rwork: 0.257

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