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

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Basic information

Entry
Database: PDB / ID: 2yib
TitleStructure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus
Components(RNA-DIRECTED RNA POLYMERASE) x 2
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: 3.8 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: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)370,8974
Polymers370,8974
Non-polymers00
Water00
1
A: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)95,6321
Polymers95,6321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)95,6321
Polymers95,6321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)95,6321
Polymers95,6321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)84,0001
Polymers84,0001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.740, 195.450, 197.380
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 / RDRP / PROTEIN VP1


Mass: 95632.492 Da / Num. of mol.: 3
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: Protein RNA-DIRECTED RNA POLYMERASE / RDRP / PROTEIN VP1


Mass: 83999.883 Da / Num. of mol.: 1
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
Sequence detailsGIVEN THE LOW RESOLUTION OF THE DIFFRACTION DATA THE AUTHORS WERE UNABLE TO RELIABLY BUILD A MAIN ...GIVEN THE LOW RESOLUTION OF THE DIFFRACTION DATA THE AUTHORS WERE UNABLE TO RELIABLY BUILD A MAIN CHAIN INTO THE DENSITY AND DOCK THE SEQUENCE FROM RESIDUE 688 ONWARDS IN CHAIN D. THE AUTHORS HAVE THEREFORE EXCLUDED THIS REGION OF THE STRUCTURE FROM THE REFINEMENT, THE COORDINATES FOR THIS SEGMENT HAVING ZERO OCCUPANCY AND NO ASSIGNED RESIDUE TYPE TO INDICATE THIS FACT.

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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: 3.02 Å3/Da / Density % sol: 63.66 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: CRYSTALS OF FULL-LENGTH VP1 WERE GROWN IN SITTING DROPS CONTAINING 100 NL PROTEIN (5.3 MG/ML) PLUS 5 MM MNCL2 AND 100 NL RESERVOIR SOLUTION (20% W/V PEG3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0. ...Details: CRYSTALS OF FULL-LENGTH VP1 WERE GROWN IN SITTING DROPS CONTAINING 100 NL PROTEIN (5.3 MG/ML) PLUS 5 MM MNCL2 AND 100 NL RESERVOIR SOLUTION (20% W/V PEG3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM CITRATE, 20 MM ATP, 5% V/V MPD, 10 MM NAOH) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.8→45.24 Å / Num. obs: 45508 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 51.01 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 4.5
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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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: 3.8→44.43 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.8795 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES D688 TO 770, CORE SEGMENT OF CHAIN D, COULD NOT BE DOCKED INTO SEQUENCE. AS SUCH THEY WERE OMITTED FROM REFINEMENT AND ARE SHOWN FOR ILLUSTRATIVE PURPOSES ONLY. IDEAL-DIST CONTACT ...Details: RESIDUES D688 TO 770, CORE SEGMENT OF CHAIN D, COULD NOT BE DOCKED INTO SEQUENCE. AS SUCH THEY WERE OMITTED FROM REFINEMENT AND ARE SHOWN FOR ILLUSTRATIVE PURPOSES ONLY. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2307 5.07 %RANDOM
Rwork0.1843 ---
obs0.1858 45473 --
Displacement parametersBiso mean: 99.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.9344 Å20 Å20 Å2
2--6.3521 Å20 Å2
3----8.2865 Å2
Refine analyzeLuzzati coordinate error obs: 0.735 Å
Refinement stepCycle: LAST / Resolution: 3.8→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24183 0 0 0 24183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00924304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0833097HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8321SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes623HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3461HARMONIC5
X-RAY DIFFRACTIONt_it24304HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion16.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28468SEMIHARMONIC4
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2508 169 5.04 %
Rwork0.2175 3181 -
all0.2192 3350 -
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)
10.69370.08340.30930.9197-0.04950.5113-0.0239-0.02490.02810.0082-0.05490.0138-0.03340.01710.0788-0.07810.0801-0.0079-0.09070.0234-0.0345-40.203932.7753-9.6447
23.5129-1.6931-1.54853.32932.91041.92420.04970.21330.1599-0.01160.0553-0.02710.003-0.012-0.1050.03540.0444-0.1076-0.11360.1405-0.0146-25.554416.24311.194
30.2334-0.34820.16250.9144-0.40161.06530.02110.01660.20060.0347-0.1336-0.1431-0.0067-0.05690.1125-0.02460.0016-0.0472-0.02570.0871-0.0189-38.469554.4351-17.8565
40.88260.53480.06460.72790.33631.95520.14240.1251-0.2398-0.02720.0510.0350.4593-0.5442-0.1934-0.0383-0.152-0.1009-0.11350.152-0.0024-44.0694-31.149610.8365
52.901-0.62591.01533.6954-2.53050.71110.0282-0.04670.0016-0.06530.03490.10180.0203-0.0396-0.0631-0.094-0.0579-0.0420.01210.05270.0425-42.6832-9.164323.5339
60.18681.06110.42921.10020.23690.61510.02250.1105-0.0866-0.2660.13580.21690.1966-0.4213-0.15830.1274-0.152-0.1520.17170.1520.1265-58.398-41.16332.7985
71.27440.071-0.53190.5292-0.38641.2786-0.1284-0.0403-0.2978-0.126-0.0737-0.26330.1454-0.05650.202-0.0541-0.01010.092-0.20050.10970.02031.353411.03535.4393
83.82431.40540.62981.0249-1.78480.7504-0.0058-0.2022-0.32360.0264-0.0191-0.1151-0.06610.00060.025-0.10920.05780.0542-0.07090.1520.08-8.0532-2.860555.6191
91.71270.3155-0.24340.404-0.05330.54790.02140.0543-0.3842-0.2073-0.1543-0.35450.18150.20140.1329-0.03960.13770.152-0.12550.15060.101821.588.80830.8417
101.4-0.09290.58970.1718-0.04240.5054-0.01740.5328-0.20780.14270.02690.01590.1668-0.1142-0.0094-0.24940.05720.0860.304-0.152-0.0632-51.8712-5.145654.053
112.8526-0.46090.90140.6717-0.16262.0619-0.07250.54420.09420.19-0.05310.2472-0.1905-0.27240.1256-0.26530.04830.02130.08220.1097-0.1414-62.463815.5965.0535
122.9602-2.9104-2.54911.9511.36843.55110.02250.05540.08690.04980.10110.0724-0.12630.0733-0.1236-0.0924-0.0857-0.05360.02230.152-0.013-38.395914.900775.6406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:581)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 582:675)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 676:798)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 3:581)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 582:657)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 658:798)
7X-RAY DIFFRACTION7CHAIN C AND (RESID 3:515)
8X-RAY DIFFRACTION8CHAIN C AND (RESID 516:671)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 672:798)
10X-RAY DIFFRACTION10CHAIN D AND (RESID 3:116)
11X-RAY DIFFRACTION11CHAIN D AND (RESID 117:599)
12X-RAY DIFFRACTION12CHAIN D AND (RESID 600:687)

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