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

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Basic information

Entry
Database: PDB / ID: 1khw
TitleCrystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology
Function and homology information


calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity ...calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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 / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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 / Helix non-globular / Special / 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 / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / 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 / MAD / Resolution: 2.7 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 1.1Apr 27, 2008Group: 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.classification / _software.name / _software.version
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)115,8836
Polymers115,6632
Non-polymers2204
Water79344
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9413
Polymers57,8311
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9413
Polymers57,8311
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.694, 119.845, 159.498
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, sodium HEPES, manganese chloride glycerol, hexanediol, 3'-deoxy-ATP, 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: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2001 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 37963 / Num. obs: 37963 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 17.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3733 / Rsym value: 0.722 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 219584
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→31.16 Å / SU ML: 250.143 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.1 / ESU R Free: 0.358 / Stereochemistry target values: Engh & Huber
Details: Grouped TLS refinement was used, with individual domains refined as a single group.
RfactorNum. reflection% reflectionSelection details
Rfree0.26747 3795 10 %RANDOM
Rwork0.23789 ---
all0.241 38016 --
obs0.24081 34165 100 %-
Displacement parametersBiso mean: 28.407 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---2.07 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7776 0 4 44 7824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217950
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9610763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1613987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.422151445
X-RAY DIFFRACTIONr_chiral_restr0.0990.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.33675
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.5497
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.336
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.11624939
X-RAY DIFFRACTIONr_mcangle_it1.9052.57970
X-RAY DIFFRACTIONr_scbond_it2.6233.53011
X-RAY DIFFRACTIONr_scangle_it4.1194.52793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 281 -
Rwork0.288 --
obs-2765 99 %
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)
111.1637-0.8847-2.26321.9202-0.14873.0609-0.34761.3420.6346-0.30840.05720.12630.1658-0.41620.29030.2381-0.1187-0.16940.40290.34270.5539.608382.44951.4684
22.5742-1.07591.27783.6111-0.70492.234-0.0814-0.09460.34440.11310.12510.1271-0.1455-0.2235-0.04370.0499-0.0617-0.04810.14990.09580.110511.248769.454920.446
35.0410.20941.49184.6693-0.35572.6116-0.03450.564-0.4207-1.07450.0726-0.31390.60210.2693-0.0380.3951-0.0472-0.02720.13270.02430.033421.592751.38947.4596
45.59414.0705-2.64858.2504-4.47663.5638-0.10830.45560.2792-0.44020.1033-0.51080.3529-0.08730.0050.08280.01170.10480.31650.24610.38136.760776.03131.2335
58.55910.44961.797615.36981.24220.8948-0.57640.04150.3256-1.05910.48510.4514-0.1216-0.18550.09130.3386-0.0118-0.07250.2873-0.02990.031333.226578.421739.2672
62.70240.02890.16476.33140.38842.8205-0.1708-0.5756-0.33611.31670.4461-0.54320.39130.1207-0.27530.47680.1499-0.20850.3193-0.02150.098337.375267.464858.4862
78.69461.2661-0.280810.25022.09441.5259-0.03070.0903-1.30460.07160.6179-2.99020.06180.8422-0.58720.41720.3371-0.37150.6913-0.40061.415760.931663.712352.9588
85.2624-0.39562.39926.8140.68173.56190.0376-0.0529-0.516-0.03540.5272-1.11350.09840.3577-0.56480.16830.0474-0.05410.1805-0.20540.331954.793192.937549.6469
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
Lowest resolution: 31.2 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.235 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.25
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: 0.318 / Rfactor Rwork: 0.288

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