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- PDB-2w69: Influenza polymerase fragment -

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Basic information

Entry
Database: PDB / ID: 2w69
TitleInfluenza polymerase fragment
ComponentsPOLYMERASE ACIDIC PROTEIN
KeywordsTRANSCRIPTION / RNA-DEPENDENT / RNA POLYMERASE
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
: / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsDias, A. / Bouvier, D. / Crepin, T. / McCarthy, A.A. / Hart, D.J. / Baudin, F. / Cusack, S. / Ruigrok, R.W.H.
CitationJournal: Nature / Year: 2009
Title: The CAP-Snatching Endonuclease of Influenza Virus Polymerase Resides in the Pa Subunit
Authors: Dias, A. / Bouvier, D. / Crepin, T. / Mccarthy, A.A. / Hart, D.J. / Baudin, F. / Cusack, S. / Ruigrok, R.W.H.
History
DepositionDec 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: POLYMERASE ACIDIC PROTEIN
B: POLYMERASE ACIDIC PROTEIN
D: POLYMERASE ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,94516
Polymers75,9023
Non-polymers1,04313
Water2,720151
1
A: POLYMERASE ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6035
Polymers25,3011
Non-polymers3024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6445
Polymers25,3011
Non-polymers3434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: POLYMERASE ACIDIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6996
Polymers25,3011
Non-polymers3985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.130, 67.130, 302.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETCYSCYS1AA1 - 88 - 15
211METMETCYSCYS1BB1 - 88 - 15
121METMETALAALA1AA12 - 1719 - 24
221METMETALAALA1BB12 - 1719 - 24
131ASNASNCYSCYS1AA33 - 4540 - 52
231ASNASNCYSCYS1BB33 - 4540 - 52
141TYRTYRARGARG1AA110 - 116117 - 123
241TYRTYRARGARG1BB110 - 116117 - 123
151VALVALLEULEU1AA122 - 132129 - 139
251VALVALLEULEU1BB122 - 132129 - 139
161HISHISPHEPHE1AA144 - 150151 - 157
261HISHISPHEPHE1BB144 - 150151 - 157
171GLUGLULEULEU1AA154 - 163161 - 170
271GLUGLULEULEU1BB154 - 163161 - 170
181ARGARGARGARG1AA174 - 192181 - 199
281ARGARGARGARG1BB174 - 192181 - 199
112ASNASNCYSCYS2BB33 - 4540 - 52
212ASNASNCYSCYS2DC33 - 4540 - 52
122GLYGLYGLUGLU2BB121 - 133128 - 140
222GLYGLYGLUGLU2DC121 - 133128 - 140
132HISHISPHEPHE2BB144 - 150151 - 157
232HISHISPHEPHE2DC144 - 150151 - 157
142TYRTYRASPASP2BB161 - 164168 - 171
242TYRTYRASPASP2DC161 - 164168 - 171
152ARGARGALAALA2BB168 - 183175 - 190
252ARGARGALAALA2DC168 - 183175 - 190

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999084, 0.018206, -0.038729), (0.042701, -0.483982, 0.874036), (-0.002831, -0.874889, -0.484316)-19.164, -38.382, 171.137
2given(0.996557, -0.082915, 0.000361), (-0.040548, -0.491132, -0.870141), (0.072325, 0.86713, -0.492802)24.6072, 129.4225, 117.8326

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Components

#1: Protein POLYMERASE ACIDIC PROTEIN / INFLUENZA POLYMERASE PA SUBUNIT / RNA-DIRECTED RNA POLYMERASE SUBUNIT P2


Mass: 25300.637 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/1975 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL CODONPLUS / References: UniProt: P31343
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GMGSGMA AT N-TERMINUS

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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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN SOLUTION WAS AT 5-10 MG.ML-1 IN 20 MM TRIS-HCL PH 8.0, 100 MM NACL, 2.5 MM MNCL2. THE RESERVOIR COMPOSITION WAS 100 MM MES PH 6.0, 1.2 M LI2SO4, 10 MM MG ACETATE, 3 % ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 41831 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 4.84 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.6
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.64 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.05→75.81 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.611 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2118 5.1 %RANDOM
Rwork0.217 ---
obs0.22 39713 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.05→75.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 45 151 4917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224869
X-RAY DIFFRACTIONr_bond_other_d0.0020.023354
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9466555
X-RAY DIFFRACTIONr_angle_other_deg0.98138117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57623.977259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06915895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571537
X-RAY DIFFRACTIONr_chiral_restr0.0810.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021043
X-RAY DIFFRACTIONr_nbd_refined0.2150.21019
X-RAY DIFFRACTIONr_nbd_other0.1940.23369
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22308
X-RAY DIFFRACTIONr_nbtor_other0.0840.22563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5923179
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24734635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42622210
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.97431918
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1143tight positional0.060.05
12B1143tight positional0.060.05
21B317tight positional0.040.05
22D317tight positional0.040.05
21B443medium positional0.240.5
22D443medium positional0.240.5
11A1143tight thermal0.170.5
12B1143tight thermal0.170.5
21B317tight thermal0.180.5
22D317tight thermal0.180.5
21B443medium thermal0.692
22D443medium thermal0.692
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 169
Rwork0.278 3094
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)
12.60681.06120.0152.0135-0.15272.5508-0.10010.2362-0.0361-0.12370.16580.07840.083-0.25-0.06570.034-0.01930.02980.1320.0543-0.04520.43831.92284.534
22.85760.1958-0.83972.1021-0.38743.10670.0073-0.27650.21330.01890.088-0.14810.00120.2691-0.09530.04040.0210.03030.0842-0.0277-0.060422.53942.142102.741
32.54830.01170.04982.07670.67328.2665-0.2912-0.3117-0.24840.2341-0.4001-0.12320.6684-0.32910.69130.157-0.08690.1110.1217-0.0160.1402-22.47720.893102.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 196
2X-RAY DIFFRACTION1A301 - 402
3X-RAY DIFFRACTION2B0 - 196
4X-RAY DIFFRACTION2B301 - 403
5X-RAY DIFFRACTION3D0 - 196
6X-RAY DIFFRACTION3D301 - 403

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