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- PDB-8iic: Crystal structure of Israeli acute paralysis virus RNA-dependent ... -

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Basic information

Entry
Database: PDB / ID: 8iic
TitleCrystal structure of Israeli acute paralysis virus RNA-dependent RNA polymerase delta40 mutant (residues 41-546)
ComponentsPolymerase polyprotein
KeywordsTRANSFERASE / RNA-dependent RNA Polymerase
Biological speciesIsraeli acute paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsFang, X. / Lu, G. / Hou, C. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
National Natural Science Foundation of China (NSFC)31802147 China
CitationJournal: Virol Sin / Year: 2023
Title: Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding.
Authors: Fang, X. / Lu, G. / Deng, Y. / Yang, S. / Hou, C. / Gong, P.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase polyprotein
B: Polymerase polyprotein


Theoretical massNumber of molelcules
Total (without water)120,5932
Polymers120,5932
Non-polymers00
Water1086
1
A: Polymerase polyprotein


Theoretical massNumber of molelcules
Total (without water)60,2971
Polymers60,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase polyprotein


Theoretical massNumber of molelcules
Total (without water)60,2971
Polymers60,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.926, 167.926, 218.321
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 56 through 57 or (resid 58...
21(chain B and (resid 56 through 67 or resid 95...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILE(chain A and (resid 56 through 57 or (resid 58...AA56 - 5734 - 35
12ARGARGHISHIS(chain A and (resid 56 through 57 or (resid 58...AA58 - 6336 - 41
13ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
14ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
15ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
16ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
17ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
18ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
19ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
110ASPASPMETMET(chain A and (resid 56 through 57 or (resid 58...AA56 - 54634 - 524
21ASPASPSERSER(chain B and (resid 56 through 67 or resid 95...BB56 - 6734 - 45
22LYSLYSTYRTYR(chain B and (resid 56 through 67 or resid 95...BB95 - 13373 - 111
23GLUGLUGLUGLU(chain B and (resid 56 through 67 or resid 95...BB134112
24THRTHRMETMET(chain B and (resid 56 through 67 or resid 95...BB55 - 54633 - 524
25THRTHRMETMET(chain B and (resid 56 through 67 or resid 95...BB55 - 54633 - 524
26THRTHRMETMET(chain B and (resid 56 through 67 or resid 95...BB55 - 54633 - 524
27THRTHRMETMET(chain B and (resid 56 through 67 or resid 95...BB55 - 54633 - 524

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Components

#1: Protein Polymerase polyprotein


Mass: 60296.715 Da / Num. of mol.: 2 / Mutation: N510D
Source method: isolated from a genetically manipulated source
Details: GB:MG599488.1 / Source: (gene. exp.) Israeli acute paralysis virus / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.25→23.8 Å / Num. obs: 28880 / % possible obs: 98.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Χ2: 0.885 / Net I/σ(I): 8.4 / Num. measured all: 295009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.3710.50.84128580.9570.2660.8830.90899.5
3.37-3.510.20.51428410.9840.1650.5410.92999.6
3.5-3.6610.30.35728400.9880.1140.3750.95299.3
3.66-3.8510.60.24328330.9920.0770.2551.00999.2
3.85-4.0910.40.16128780.9950.0520.1690.99999.3
4.09-4.41100.11128590.9960.0370.1170.95898.8
4.41-4.8510.50.08628780.9970.0270.090.84498.9
4.85-5.549.90.06828930.9970.0230.0720.71798.7
5.54-6.9510.30.05229360.9980.0170.0540.73998.2
6.95-23.89.40.02830640.9990.0090.0290.78897.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IIB

8iib


Resolution: 3.25→23.78 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1401 5.05 %
Rwork0.2113 26335 -
obs0.2131 27736 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.22 Å2 / Biso mean: 51.2462 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 3.25→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 6 6070
Biso mean---33.38 -
Num. residues----808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2284X-RAY DIFFRACTION9.53TORSIONAL
12B2284X-RAY DIFFRACTION9.53TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.370.29551000.26431830193067
3.37-3.50.34281460.26132506265293
3.5-3.660.28151460.24332680282699
3.66-3.850.2591360.22552701283799
3.85-4.090.25311390.20442737287699
4.09-4.410.23191510.18692703285499
4.41-4.850.20891570.17952724288199
4.85-5.540.23361370.19652751288899
5.54-6.950.25021340.23242804293898
6.95-23.780.21971550.19982899305497

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