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- PDB-5fsw: RNA dependent RNA polymerase QDE-1 from Thielavia terrestris -

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Basic information

Entry
Database: PDB / ID: 5fsw
TitleRNA dependent RNA polymerase QDE-1 from Thielavia terrestris
ComponentsRNA DEPENDENT RNA POLYMERASE QDE-1
KeywordsTRANSFERASE / SMALL RNAS / QDE-1 ORTHOLOGUES / EVOLUTION
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / siRNA processing / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
RNA-dependent RNA polymerase, slab domain, helical subdomain-like / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesTHIELAVIA TERRESTRIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsQian, X. / Hamid, F.M. / El Sahili, A. / Darwis, D.A. / Wong, Y.H. / Bhushan, S. / Makeyev, E.V. / Lescar, J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Functional Evolution in Orthologous Cell-Encoded RNA-Dependent RNA Polymerases
Authors: Qian, X. / Hamid, F.M. / El Sahili, A. / Darwis, D.A. / Wong, Y.H. / Bhushan, S. / Makeyev, E.V. / Lescar, J.
History
DepositionJan 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A -9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA DEPENDENT RNA POLYMERASE QDE-1
B: RNA DEPENDENT RNA POLYMERASE QDE-1
C: RNA DEPENDENT RNA POLYMERASE QDE-1
D: RNA DEPENDENT RNA POLYMERASE QDE-1


Theoretical massNumber of molelcules
Total (without water)464,2354
Polymers464,2354
Non-polymers00
Water00
1
A: RNA DEPENDENT RNA POLYMERASE QDE-1
B: RNA DEPENDENT RNA POLYMERASE QDE-1


Theoretical massNumber of molelcules
Total (without water)232,1182
Polymers232,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-48.2 kcal/mol
Surface area82230 Å2
MethodPISA
2
C: RNA DEPENDENT RNA POLYMERASE QDE-1
D: RNA DEPENDENT RNA POLYMERASE QDE-1


Theoretical massNumber of molelcules
Total (without water)232,1182
Polymers232,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-43.4 kcal/mol
Surface area81520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 165.950, 173.890
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 22 - 1006 / Label seq-ID: 22 - 1006

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.99961, 0.00692, 0.02697), (-0.02645, 0.06664, -0.99743), (-0.0087, -0.99775, -0.06643)64.26906, 78.77675, 83.72645
2given(-0.99953, -0.00828, -0.02939), (-0.02981, 0.05664, 0.99795), (-0.0066, 0.99836, -0.05686)4.76018, -176.00908, 186.55022

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Components

#1: Protein
RNA DEPENDENT RNA POLYMERASE QDE-1 / RDRP QDE


Mass: 116058.859 Da / Num. of mol.: 4 / Fragment: RDRP C-TERMINAL DOMAIN, UNP RESIDUES 364-1373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIELAVIA TERRESTRIS (fungus)
Description: SYNTHETIC GENE FROM AEO68606.1 FROM E364 TO D1373
Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: G2R911

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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: 2.84 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS PH8, 75 MM NACL, 10% PEG10K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 78767 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.23
Reflection shellResolution: 3.19→3.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.14 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J7N

2j7n


Resolution: 3.19→48.91 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.8 / SU B: 29.47 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25094 3829 4.8 %RANDOM
Rwork0.21297 ---
obs0.21481 75503 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.585 Å2
Baniso -1Baniso -2Baniso -3
1--7.23 Å20 Å21.53 Å2
2--9.93 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 3.19→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28130 0 0 0 28130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01928716
X-RAY DIFFRACTIONr_bond_other_d0.0090.0226584
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.95238656
X-RAY DIFFRACTIONr_angle_other_deg1.637361139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01853628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01723.2371180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.431154668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.64315227
X-RAY DIFFRACTIONr_chiral_restr0.0990.24156
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02132166
X-RAY DIFFRACTIONr_gen_planes_other0.010.026514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A465720.16
12B465720.16
21A469330.15
22C469330.15
31A466960.16
32D466960.16
41B478500.14
42C478500.14
51B480430.13
52D480430.13
61C479370.13
62D479370.13
LS refinement shellResolution: 3.19→3.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 251 -
Rwork0.14 5366 -
obs--96.21 %
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)
10.02250.0419-0.00530.2431-0.03540.00820.01740.00050.0244-0.0168-0.01580.0369-0.01490.0153-0.00160.1713-0.01280.0020.17280.00030.029516.53714.68991.311
20.1743-0.0815-0.01330.10430.01480.10860.0110.06180.0317-0.0635-0.0161-0.0077-0.0230.00560.00510.1875-0.00640.00470.14910.00950.007850.301-11.7562.867
30.0195-0.01870.02440.0299-0.02520.0341-0.00710.014-0.00070.016-0.0043-0.0096-0.01260.0010.01140.1681-0.00160.01440.2138-0.00060.061416.754-26.572178.033
40.0434-0.01360.00160.0061-0.0020.0015-0.01260.0179-0.00280.01410.011-0.0019-0.0066-0.01540.00150.2122-0.00540.00360.2148-0.00150.0361-17.009-0.338149.81
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 1006
2X-RAY DIFFRACTION2B22 - 1006
3X-RAY DIFFRACTION3C22 - 1006
4X-RAY DIFFRACTION4D22 - 1006

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