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- PDB-1n1h: Initiation complex of polymerase lambda3 from reovirus -

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Basic information

Entry
Database: PDB / ID: 1n1h
TitleInitiation complex of polymerase lambda3 from reovirus
Components
  • 5'-R(*AP*UP*UP*AP*GP*C)-3'
  • Minor core protein lambda 3
KeywordsTRANSFERASE/RNA / polymerase / initiation complex / right hand configuration / TRANSFERASE-RNA COMPLEX
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
3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE / N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3
Similarity search - Component
Biological speciesMammalian orthoreovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 [lambda] 3
Authors: Tao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(*AP*UP*UP*AP*GP*C)-3'
A: Minor core protein lambda 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2068
Polymers144,3002
Non-polymers1,9066
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.883, 85.013, 249.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain 5'-R(*AP*UP*UP*AP*GP*C)-3'


Mass: 1876.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AUUAGC, RNA oligo ordered from Dharmacon
#2: Protein Minor core protein lambda 3 / lambda3


Mass: 142423.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Dearing / Gene: L1 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P17378, UniProt: P0CK31*PLUS

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Non-polymers , 6 types, 189 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-G7M / N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 378.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O8P
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-CH1 / 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#7: Chemical ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
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
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaClSodium chloride11
3HEPES11
4glycerol11
5PEG 400012
6NaClSodium chloride12
7glycerol12
8HEPES12
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: 19-ID / Wavelength: 1.03 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 30558 / Num. obs: 30558 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2846 / % possible all: 75.6
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 2-3 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 75.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: lambda3 native structure

Resolution: 2.8→29.71 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1794 5.9 %RANDOM
Rwork0.216 ---
all0.219 30191 --
obs0.216 30191 79.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.4353 Å2 / ksol: 0.365407 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å20 Å2
2---2.17 Å20 Å2
3---5.07 Å2
Refine analyzeLuzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9986 86 113 183 10368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 128 4.5 %
Rwork0.276 2700 -
obs--75.9 %
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_NTP_DEOXY_XPLOR.PARMGP_NTP_DEOXY_XPLOR.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.395
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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