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- PDB-2yi9: Structure of the RNA polymerase VP1 from Infectious Pancreatic Ne... -

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Basic information

Entry
Database: PDB / ID: 2yi9
TitleStructure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus in complex with magnesium
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: 2.2 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 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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)448,41321
Polymers447,8835
Non-polymers53016
Water53,8472989
1
A: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6754
Polymers89,5771
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6754
Polymers89,5771
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6754
Polymers89,5771
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6754
Polymers89,5771
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7115
Polymers89,5771
Non-polymers1344
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 2989 / 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 growTemperature: 293.65 K / Method: 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 DEGREES CELSIUS. CRYSTALS WERE SOAKED BY DILUTING THE MOTHER-LIQUOR WITH APPROX. 0.5 UL 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25 AND 20% V/V GLYCEROL, TRANSFERRING THE CRYSTALS TO A FRESH DROP CONTAINING 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25, 20% V/V GLYCEROL, 50 MM MGCL2 AND 10 UM GTP, AND INCUBATING FOR 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: 2.2→101.81 Å / Num. obs: 304685 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.03 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / % 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: 2.2→32.21 Å / Cor.coef. Fo:Fc: 0.9493 / Cor.coef. Fo:Fc free: 0.9449 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 3069 1.01 %RANDOM
Rwork0.1603 ---
obs0.1605 304439 100 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.3797 Å20 Å20 Å2
2---1.5091 Å20 Å2
3---0.1295 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30143 0 16 2989 33148
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01130969HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9842196HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10710SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes791HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4444HARMONIC5
X-RAY DIFFRACTIONt_it30969HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion15.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4174SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies29HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37694SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2222 246 1.1 %
Rwork0.1903 22029 -
all0.1907 22275 -
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)
10.90960.1620.03980.4133-0.07710.31950.007-0.1408-0.023-0.0201-0.01730.02740.0136-0.03240.0103-0.0962-0.0047-0.01520.00010.0047-0.11676.6337-24.1917-6.6575
20.4846-0.0016-0.35830.20070.02750.69240.0520.04820.0424-0.01490.02150.0165-0.0821-0.0337-0.0735-0.05820.0010.0205-0.05310.0128-0.072560.274419.1701-11.2739
30.7363-0.1155-0.31860.49-0.01430.4750.0707-0.06060.036-0.01350.01130.0109-0.0618-0.0329-0.082-0.0750.00040.0121-0.0831-0.0049-0.0818-20.36327.6964-54.065
40.6384-0.00160.11480.46550.05330.3670.0099-0.005-0.012-0.02250.0075-0.0020.0052-0.0278-0.0174-0.0740.0028-0.0065-0.0720.0112-0.070587.3592-42.3635-46.4489
50.3756-0.08490.15610.2861-0.06060.35480.00030.01660.01240.0042-0.00010.00680.01020.0217-0.0002-0.047-0.0034-0.0028-0.05290.0113-0.053332.7317-11.0926-75.0785
60.2485-0.06420.50440.5251-0.55390.5011-0.0146-0.0424-0.00870.07980.007-0.041-0.0072-0.02570.00760.02920.01210.0182-0.04510.08660.000917.085-19.8015-63.2798
70.13280.44810.61940.13810.38661.0841-0.0075-0.01820.03250.0465-0.03640.0068-0.03110.0330.044-0.02460.0619-0.03560.1044-0.0299-0.087171.867-35.925-33.3109
80.08230.229-0.15380.481-0.48970.159-0.00350.0150.0343-0.03090.0032-0.0086-0.02110.00750.00040.0150.0274-0.1192-0.0598-0.03650.037-9.5118-10.0883-8.9728
90.33-0.3701-0.04840.82960.4890-0.00680.0112-0.0271-0.01260.027-0.01180.04270.0038-0.0202-0.0036-0.00250.0018-0.0607-0.06150.055497.843414.5495-60.1857
100.11050.25-0.32690.00580.26210.9988-0.00230.04210.0035-0.04030.0057-0.03070.0228-0.0239-0.00340.01680.01850.02220.10220.1049-0.125444.313521.7361-25.5233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 31-792 OR 1793)
2X-RAY DIFFRACTION2(CHAIN B AND RESIDUES 31-792 OR 1793)
3X-RAY DIFFRACTION3(CHAIN C AND RESIDUES 31-792 OR 1793)
4X-RAY DIFFRACTION4(CHAIN D AND RESIDUES 31-792 OR 1793)
5X-RAY DIFFRACTION5(CHAIN E AND RESIDUES 31-792 OR 1793)
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 DIFFRACTION9(CHAIN D AND RESIDUES 11-19)
10X-RAY DIFFRACTION10(CHAIN E AND RESIDUES 11-19)

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