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- PDB-2yi8: Structure of the RNA polymerase VP1 from Infectious Pancreatic Ne... -

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Basic information

Entry
Database: PDB / ID: 2yi8
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: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,29116
Polymers447,8835
Non-polymers40811
Water56,6213143
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6513
Polymers89,5771
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6513
Polymers89,5771
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6513
Polymers89,5771
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6513
Polymers89,5771
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6874
Polymers89,5771
Non-polymers1103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.048, 183.874, 244.521
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.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3143 / Source method: isolated from a natural source / Formula: H2O
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: 3.36 Å3/Da / Density % sol: 63.44 % / 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 PEG 3350, 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 PEG 3350, 0.10-0.09 M BIS-TRIS PROPANE PH 7.5, 0.2-0.18 M SODIUM CITRATE) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 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: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→92.13 Å / Num. obs: 268352 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 23.34 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % 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 2PGG

2pgg


Resolution: 2.3→90.33 Å / Cor.coef. Fo:Fc: 0.9328 / Cor.coef. Fo:Fc free: 0.9246 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 2655 1 %RANDOM
Rwork0.1661 ---
obs0.1663 266799 100 %-
Displacement parametersBiso mean: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.646 Å20 Å20 Å2
2---2.0546 Å20 Å2
3---2.7006 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: LAST / Resolution: 2.3→90.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30154 0 11 3143 33308
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01131029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0342286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10756SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes786HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4464HARMONIC5
X-RAY DIFFRACTIONt_it31029HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion15.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4184SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies37HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact38474SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2125 190 0.97 %
Rwork0.1944 19348 -
all0.1946 19538 -
obs--100 %
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)
10.84060.14790.06240.3265-0.08150.31370.0058-0.1161-0.0216-0.0216-0.01960.01510.0152-0.02170.0137-0.081-0.0061-0.01220.00260.0075-0.0996.5133-24.3606-6.7491
20.4854-0.0229-0.34120.1420.04820.59930.03440.04250.0452-0.01880.03450.0015-0.0745-0.0323-0.0689-0.0475-0.00440.0292-0.04750.015-0.053860.139418.8364-11.3815
30.6703-0.0844-0.25940.4411-0.06230.38540.0807-0.05230.0326-0.0087-0.00610.0027-0.0496-0.0207-0.0746-0.05920.00030.0154-0.08720.0009-0.066-20.42327.3926-53.9594
40.62-0.00230.08410.40030.02160.3378-0.010.0142-0.0136-0.03520.0147-0.01670.0177-0.025-0.0047-0.0656-0.0084-0.0044-0.06850.0107-0.068387.2486-42.4907-46.4381
50.3462-0.07960.09850.2596-0.06690.3129-0.00680.02080.00480.0030.00330.0122-0.03440.02950.0035-0.03680.0088-0.0074-0.06630.015-0.065132.7395-11.1225-75.0527
60.0041-0.02840.04330.0364-0.12580.0556-0.0007-0.003-0.00190.0050.002-0.00170.00110.0017-0.00130.01380.00730.0034-0.01130.0362-0.00317.0543-19.9636-63.463
70.01640.02150.094800.1620.1648-0.0012-0.00340.0030.0031-0.0031-0.0019-0.00520.0030.0043-0.0030.0138-0.01450.0239-0.017-0.020171.7767-36.1467-33.2632
80.00720.05-0.00110.0604-0.09810.0073-0.00060.00180.0038-0.00050.0011-0.0017-0.00340.0006-0.00060.00130.0048-0.0268-0.0078-0.00020.0066-9.5793-10.2821-9.0821
90.0564-0.0891-0.03220.1070.12890-0.00090.0011-0.0035-0.00020.00260.00150.00330.002-0.0017-0.0046-0.00130.0074-0.0148-0.02820.019397.825614.3667-60.2415
100.00620.0165-0.05080-0.06350.0992-0.00040.0036-0.0006-0.00380.0008-0.00260.001-0.0014-0.00040.00660.00270.00720.01530.0257-0.021744.303121.3351-25.6528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 31-792)
2X-RAY DIFFRACTION2(CHAIN B AND RESIDUES 31-792)
3X-RAY DIFFRACTION3(CHAIN C AND RESIDUES 31-792)
4X-RAY DIFFRACTION4(CHAIN D AND RESIDUES 31-792)
5X-RAY DIFFRACTION5(CHAIN E AND RESIDUES 31-792)
6X-RAY DIFFRACTION6(CHAIN A AND RESIDUES 11-19)
7X-RAY DIFFRACTION7(CHAIN B AND RESIDUES 11-19)
8X-RAY DIFFRACTION8(CHAIN C AND RESIDUES 11-19)
9X-RAY DIFFRACTION9CHAIN D AND RESIDUES 11-19)
10X-RAY DIFFRACTION10(CHAIN E AND RESIDUES 11-19)

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