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- PDB-4nfz: Crystal structure of polymerase subunit PA N-terminal endonucleas... -

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Basic information

Entry
Database: PDB / ID: 4nfz
TitleCrystal structure of polymerase subunit PA N-terminal endonuclease domain from bat-derived influenza virus H17N10
ComponentsPolymerase PA
KeywordsRNA BINDING PROTEIN / RNA endonuclease / Manganese Binding
Function / homology
Function and homology information


viral translational frameshifting / viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTefsen, B. / Lu, G. / Zhu, Y. / Haywood, J. / Zhao, L. / Deng, T. / Qi, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2014
Title: The N-Terminal Domain of PA from Bat-Derived Influenza-Like Virus H17N10 Has Endonuclease Activity
Authors: Tefsen, B. / Lu, G. / Zhu, Y. / Haywood, J. / Zhao, L. / Deng, T. / Qi, J. / Gao, G.F.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Polymerase PA
B: Polymerase PA
C: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6756
Polymers76,5103
Non-polymers1653
Water39622
1
A: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5582
Polymers25,5031
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5582
Polymers25,5031
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5582
Polymers25,5031
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Polymerase PA
hetero molecules

B: Polymerase PA
hetero molecules

A: Polymerase PA
C: Polymerase PA
hetero molecules

A: Polymerase PA
C: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,35012
Polymers153,0216
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation12_445x-1,x-y-1,-z+1/61
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area7890 Å2
ΔGint-57 kcal/mol
Surface area56660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.300, 74.300, 401.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Polymerase PA


Mass: 25503.424 Da / Num. of mol.: 3 / Fragment: UNP residues 1-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)
Gene: PA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H6QM92
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 0.1M sodium chloride, 0.1M Bis-Tris, 1.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.699→50 Å / Num. obs: 19269 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 15.6 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 27.69
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.654 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W69

2w69


Resolution: 2.7→42.8 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 988 5.14 %
Rwork0.24 --
obs0.242 19228 99.9 %
all-19228 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 3 22 4927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135001
X-RAY DIFFRACTIONf_angle_d1.5516723
X-RAY DIFFRACTIONf_dihedral_angle_d19.6551902
X-RAY DIFFRACTIONf_chiral_restr0.099699
X-RAY DIFFRACTIONf_plane_restr0.007885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.699-2.84150.35761410.31652518X-RAY DIFFRACTION100
2.8415-3.01950.34451320.29232516X-RAY DIFFRACTION100
3.0195-3.25250.37331250.28652567X-RAY DIFFRACTION100
3.2525-3.57970.32051470.26712565X-RAY DIFFRACTION100
3.5797-4.09730.24791700.22892564X-RAY DIFFRACTION100
4.0973-5.16080.22621330.20142642X-RAY DIFFRACTION100
5.1608-42.80110.26261400.22112868X-RAY DIFFRACTION99
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)
10.9111-1.19250.05773.6861-0.3792.0430.0779-0.09440.12960.70550.11170.29950.0076-0.12790.01870.3924-0.01070.01120.23430.01280.266736.71211.357418.4183
21.42941.5897-0.10283.52690.59262.3759-0.1237-0.19710.10270.3372-0.04730.56650.1757-0.060.08840.37360.04030.02110.3418-0.02290.379230.564-7.873225.5554
31.9570.46780.40212.7191-0.09342.0401-0.26590.2105-0.3127-0.64130.1521-1.02630.70540.73450.08830.48230.12580.09110.49490.0730.47946.5126-7.074715.6303
41.74230.3641-1.01234.9155-0.76222.7886-0.03540.4480.1718-0.69340.2706-0.29850.19420.1956-0.0120.4448-0.02760.00610.3987-0.03840.263840.82914.8176.0621
52.54750.96020.07663.05590.04023.8319-0.07190.3604-0.469-0.2224-0.28030.10140.1863-0.0750.00180.33690.0426-0.00350.4158-0.06220.546737.20937.956849.3788
63.93932.41430.3744.1143-1.41461.74780.0951-0.3260.40650.2858-0.14020.5307-0.342-0.0785-0.05150.3062-0.0136-0.00780.3275-0.10130.383449.684224.438251.3334
72.6332-0.46460.54123.0004-0.71711.9082-0.22110.0716-0.3436-0.29610.2312-0.28470.17190.0537-0.0010.269-0.00740.05390.3757-0.0640.349755.180515.490140.222
80.5389-0.1078-1.17342.33290.03132.794-0.042-0.8514-0.87140.2357-0.0176-0.47740.17820.52031.0960.26540.0085-0.14210.51820.32520.552154.61958.442757.3452
91.71610.24410.53173.3017-0.33892.691-0.17370.20860.6123-0.31020.21790.1544-0.39210.49380.00860.3833-0.02470.04510.44070.03060.43420.54246.895655.9689
101.9872-0.4478-1.94635.71120.78932.5896-0.22790.21370.128-0.12960.01820.02550.08460.04090.09450.34660.0004-0.03430.32230.00410.344925.3521-10.119645.9631
112.60060.03630.12712.15460.17282.7271-0.08240.3110.0086-0.00610.05881.17490.0175-0.36850.08920.6297-0.10240.12820.5659-0.02520.671110.4071-12.046553.8001
121.3367-0.45990.13834.22482.52992.4630.2542-0.3986-0.330.9529-0.29841.19650.5464-0.38870.02540.8584-0.03440.19910.45330.01830.520515.5464-1.793866.5574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 196 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 31 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 75 )
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 149 )
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 196 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 49 )
10X-RAY DIFFRACTION10chain 'C' and (resid 50 through 126 )
11X-RAY DIFFRACTION11chain 'C' and (resid 127 through 164 )
12X-RAY DIFFRACTION12chain 'C' and (resid 165 through 196 )

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