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- PDB-2yia: Structure of the RNA polymerase VP1 from Infectious Pancreatic Ne... -

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Basic information

Entry
Database: PDB / ID: 2yia
TitleStructure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / REVERSE TRANSCRIPTASE / IPNV
Function / homology
Function and homology information


viral genome replication / virion component / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding
Similarity search - Function
VP1, C-terminal extension domain / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain ...VP1, C-terminal extension domain / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain / Birnavirus RNA dependent RNA polymerase (VP1), thumb domain / Birnavirus RNA dependent RNA polymerase (VP1), C-terminal / RdRp of Birnaviridae dsRNA viruses catalytic domain profile. / Helix hairpin bin / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Helix Hairpins / Helix non-globular / Special / Helix Hairpins / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesINFECTIOUS PANCREATIC NECROSIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsGraham, S.C. / Sarin, L.P. / Bahar, M.W. / Myers, R.A. / Stuart, D.I. / Bamford, D.H. / Grimes, J.M.
CitationJournal: Plos Pathog. / Year: 2011
Title: The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus is the Determinant of Genome Attachment.
Authors: Graham, S.C. / Sarin, L.P. / Bahar, M.W. / Myers, R.A. / Stuart, D.I. / Bamford, D.H. / Grimes, J.M.
History
DepositionMay 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
C: RNA-DIRECTED RNA POLYMERASE
D: RNA-DIRECTED RNA POLYMERASE
E: RNA-DIRECTED RNA POLYMERASE
F: RNA-DIRECTED RNA POLYMERASE
G: RNA-DIRECTED RNA POLYMERASE
H: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)716,92616
Polymers716,6138
Non-polymers3138
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6162
Polymers89,5771
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)200.938, 209.467, 243.393
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 / VP1 / RDRP / PROTEIN VP1


Mass: 89576.625 Da / Num. of mol.: 8 / Fragment: RESIDUES 1-790
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFECTIOUS PANCREATIC NECROSIS VIRUS / Strain: JASPER / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P22173, RNA-directed RNA polymerase, RNA-directed DNA polymerase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
Sequence detailsCONSTRUCT LACKS C-TERMINAL 55 RESIDUES AND CARRIES A HIS6 PURIFICATION TAG.

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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: 3.57 Å3/Da / Density % sol: 65.58 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING 200 NL PROTEIN (5.8-6.8 MG/ML) AND 100 NL RESERVOIR SOLUTION (20-18% W/V PEG3350, 0.10-0.09 M BIS-TRIS PROPANE PH 7.5, 0.2-0.18 M SODIUM ...Details: CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING 200 NL PROTEIN (5.8-6.8 MG/ML) AND 100 NL RESERVOIR SOLUTION (20-18% W/V PEG3350, 0.10-0.09 M BIS-TRIS PROPANE PH 7.5, 0.2-0.18 M SODIUM CITRATE) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20. C. CRYSTALS WERE CRYOPROTECTED BY SOAKING IN MOTHER-LIQUOR SUPPLEMENTED WITH 20-25% GLYCEROL FOR 1-10 MIN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.02→145.01 Å / Num. obs: 200159 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 83.8 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.6
Reflection shellResolution: 3.02→3.1 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YI9

2yi9


Resolution: 3.02→145.01 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.8922 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 2029 1.01 %RANDOM
Rwork0.1874 ---
obs0.1877 200055 --
Displacement parametersBiso mean: 65.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.4865 Å20 Å20 Å2
2--1.8511 Å20 Å2
3---3.6355 Å2
Refine analyzeLuzzati coordinate error obs: 0.575 Å
Refinement stepCycle: LAST / Resolution: 3.02→145.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49061 0 8 0 49069
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01150335HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1368572HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d17284SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1323HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7170HARMONIC5
X-RAY DIFFRACTIONt_it50335HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion16.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact57929SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2704 145 1.03 %
Rwork0.2489 13888 -
all0.2492 14033 -
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)
10.671-0.33980.22931.2995-2.81140.85390.0004-0.0252-0.01130.0350.01230.0009-0.0311-0.0021-0.01270.0564-0.0219-0.06370.0252-0.01310.053821.333764.634108.455
20.6521-0.0752-0.08431.68650.47780.71290.01810.0943-0.0612-0.2356-0.011-0.1895-0.06170.021-0.0071-0.06390.0091-0.0088-0.1111-0.0065-0.071638.621142.14963.4169
31.8628-2.10650.73810.75552.08790.40510.00580.04090.0335-0.0308-0.0013-0.0443-0.00360.0278-0.00450.05240.0469-0.07250.06280.03560.058366.807288.1456101.768
40.78560.178-0.13970.3572-0.46890.47930.0378-0.1618-0.1849-0.04190.01940.0659-0.0741-0.0636-0.0573-0.04570.0217-0.0965-0.0290.0701-0.036622.104972.1943126.165
50.66772.91040.36981.372-1.60340.9176-0.00010.00540.04270.01650.0050.056-0.0325-0.0259-0.00490.0385-0.037-0.02720.07730.01010.026930.4468109.93472.6042
60.4034-0.27220.05230.89470.22350.4061-0.027-0.0588-0.0554-0.05070.1816-0.4262-0.05660.2945-0.1546-0.2625-0.0883-0.03650.0903-0.11920.247778.753792.943287.3714
70.5611-0.25280.92690.9062-1.42410.34290.0029-0.01420.0033-0.00530.0112-0.0231-0.02140.0069-0.0140.0284-0.0001-0.0690.03960.04190.019938.22138.261114.362
81.01760.08430.43210.63540.09150.50390.03080.21590.0225-0.008-0.00460.0894-0.03550.0447-0.0262-0.0621-0.0198-0.0884-0.02870.1029-0.061412.3869116.4574.1052
90-0.33520.0661.12831.68820.4650.0025-0.00020.0188-0.02080.0010.0113-0.01070.0083-0.00350.03680.0302-0.0380.0497-0.04410.002262.1282162.1875.8154
100.5543-0.18730.39540.5144-0.43260.97650.0081-0.1283-0.08390.11650.11860.1216-0.0663-0.0493-0.12660.07740.1244-0.1123-0.0431-0.0309-0.094152.5142145.548125.022
110.0241-0.1424-0.83840.81330.332900.001-0.00190.00480.0144-0.005-0.01220.0303-0.00930.0040.02040.01790.05370.0035-0.00860.023319.3046184.72280.684
120.9243-0.1043-0.28170.68450.37330.65570.00770.25320.10830.08350.1252-0.08720.04870.136-0.1329-0.13130.03090.00790.0504-0.0362-0.093858.8984167.70257.7094
130.88920.2505-0.28760.5593-0.44810.7057-0.0534-0.14430.03970.1342-0.0386-0.05220.0314-0.0380.09210.0469-0.00180.1291-0.127-0.0791-0.0637.1981195.98299.0237
140.33320.6750.25161.79792.07790-0.0076-0.0090.0113-0.02580.00430.0087-0.0142-0.010.00330.0098-0.0138-0.06190.0177-0.01890.059151.3958246.45476.7352
151.8769-1.57951.38741.8413-1.57541.74730.0838-0.5264-0.4431-0.25810.20760.3634-0.0242-0.3457-0.2914-0.22290.1477-0.152-0.00180.10820.064767.4284229.019123.279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 3-30)
2X-RAY DIFFRACTION2(CHAIN A AND RESIDUES 31-792)
3X-RAY DIFFRACTION3(CHAIN B AND RESIDUES 3-30)
4X-RAY DIFFRACTION4(CHAIN B AND RESIDUES 31-792)
5X-RAY DIFFRACTION5(CHAIN C AND RESIDUES 3-30)
6X-RAY DIFFRACTION6(CHAIN C AND RESIDUES 31-792)
7X-RAY DIFFRACTION7(CHAIN D AND RESIDUES 3-30)
8X-RAY DIFFRACTION8(CHAIN D AND RESIDUES 31-792)
9X-RAY DIFFRACTION9(CHAIN E AND RESIDUES 3-30)
10X-RAY DIFFRACTION10(CHAIN E AND RESIDUES 31-792)
11X-RAY DIFFRACTION11(CHAIN F AND RESIDUES 11-30)
12X-RAY DIFFRACTION12(CHAIN F AND RESIDUES 31-792)
13X-RAY DIFFRACTION13(CHAIN G AND RESIDUES 31-792)
14X-RAY DIFFRACTION14(CHAIN H AND RESIDUES 3-30)
15X-RAY DIFFRACTION15(CHAIN H AND RESIDUES 31-792)

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