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- PDB-1mwh: REOVIRUS POLYMERASE LAMBDA3 BOUND TO MRNA CAP ANALOG -

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Basic information

Entry
Database: PDB / ID: 1mwh
TitleREOVIRUS POLYMERASE LAMBDA3 BOUND TO MRNA CAP ANALOG
ComponentsMINOR CORE PROTEIN LAMBDA 3
KeywordsVIRAL PROTEIN / polymerase / polymerase-cap analog complex / right hand configuration
Function / homology
Function and homology information


viral genome replication / viral nucleocapsid / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / RNA binding
Similarity search - Function
RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / : / RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3
Similarity search - Component
Biological speciesReovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: RNA Synthesis in a Cage-Structural Studies of Reovirus Polymerase lambda3
Authors: Tao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C.
History
DepositionSep 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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

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Assembly

Deposited unit
A: MINOR CORE PROTEIN LAMBDA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2823
Polymers142,4241
Non-polymers8582
Water12,088671
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.891, 84.944, 249.246
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 MINOR CORE PROTEIN LAMBDA 3


Mass: 142423.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus sp. / Gene: L1 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17378, UniProt: P0CK31*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG4000, sodium chloride, HEPES, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.7 mg/mlprotein1drop
250 mMsodium HEPES1droppH7.8
310 %glycerol1drop
4150 mM1dropNaCl
510 mMdithiothreitol1drop
60.02 %1dropNaN3
77.5 %PEG80001reservoir
810 %glycerol1reservoir
90.1 Msodium HEPES1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→49.88 Å / Num. all: 53049 / Num. obs: 49606 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5 % / Biso Wilson estimate: 42.5 Å2 / Limit h max: 28 / Limit h min: 0 / Limit k max: 34 / Limit k min: 0 / Limit l max: 99 / Limit l min: 0 / Observed criterion F max: 2281469.39 / Observed criterion F min: 19.9 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2 / Num. unique all: 4223 / % possible all: 81.7
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Redundancy: 5-6 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 80.8 % / Rmerge(I) obs: 0.404

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: reovirus polymerase 1MUK

1muk


Resolution: 2.5→49.88 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2636 5.3 %same set of reflections as used in refining the native lambda3 structure
Rwork0.209 ---
all0.243 53069 --
obs0.243 49423 93.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 33.302 Å2 / ksol: 0.364169 e/Å3
Displacement parametersBiso max: 98.19 Å2 / Biso mean: 33.69 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9930 0 53 671 10654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg22.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.2851552.40.28650710.0236524522680.1
2.61-2.750.2442313.50.24554920.0166569572387.1
2.75-2.920.2322724.10.23356830.0146572595590.6
2.92-3.150.2243625.50.22456820.0126562604492.1
3.15-3.470.2074056.10.20758480.016589625394.9
3.47-3.970.1984126.20.19761650.016643657799
3.97-50.173945.90.16963070.00967046701100
5-49.880.2184055.80.21965390.0116956694499.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4mgp.parmgp.top
X-RAY DIFFRACTION5ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.719

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