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- PDB-7kl3: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7kl3
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to RNA oligomer AG*CAUC (*uncleaveable bond, -UC disordered)
Components
  • Protein PA-X
  • RNA (5'-R(P*AP*GP*CP*A)-3')
KeywordsVIRAL PROTEIN/RNA / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / RNA oligomer / uncleaveable bond / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


viral translational frameshifting / viral RNA genome replication / nucleotide binding / RNA binding / metal ion binding
Similarity search - Function
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
ADENOSINE MONOPHOSPHATE / 5'-O-sulfocytidine / RNA / Protein PA-X / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCuypers, M.G. / Kumar, G. / White, S.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI098757 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)CA021765 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Authors: Kumar, G. / Cuypers, M. / Webby, R.R. / Webb, T.R. / White, S.W.
History
DepositionOct 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PA-X
B: RNA (5'-R(P*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9647
Polymers25,0102
Non-polymers9555
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.202, 89.202, 134.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Protein PA-X


Mass: 23134.316 Da / Num. of mol.: 1 / Mutation: E119D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA-X, PA / Variant: H1N1/PAN09/CALIFORNIA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4P2TE19, UniProt: A0A646SQW7, UniProt: A0A5J6VBC3*PLUS
#2: RNA chain RNA (5'-R(P*AP*GP*CP*A)-3')


Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GC bond uncleavable / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 125 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-RQA / 5'-O-sulfocytidine


Mass: 323.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O8S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 0.1M MGCL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 18911 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 38.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 30.5
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1369 / CC1/2: 0.807 / Rpim(I) all: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 1.99→40 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: THE UNCLEAVABLE BASE *C BEARING THE SULFUR ATOM INSTEAD OF PHOSPHATE HAS A SLIGHTLY SHORTER S-O BOND LENGTH THAN NORMAL ON THE SIDE OF THE NEIGHBORING BASE
RfactorNum. reflection% reflection
Rfree0.2097 1037 5.49 %
Rwork0.1776 17868 -
obs0.1793 18905 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.61 Å2
Refinement stepCycle: LAST / Resolution: 1.99→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 45 58 120 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01741607
X-RAY DIFFRACTIONf_angle_d1.45912181
X-RAY DIFFRACTIONf_chiral_restr0.0915234
X-RAY DIFFRACTIONf_plane_restr0.0096265
X-RAY DIFFRACTIONf_dihedral_angle_d17.4802598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.10.31311440.26652501X-RAY DIFFRACTION99.96
2.1-2.230.25961400.21932511X-RAY DIFFRACTION99.89
2.23-2.40.27491610.21362510X-RAY DIFFRACTION100
2.4-2.640.23661600.19122522X-RAY DIFFRACTION100
2.64-3.020.25561300.19822540X-RAY DIFFRACTION100
3.02-3.810.18741560.17182577X-RAY DIFFRACTION99.93
3.81-400.17511460.15292707X-RAY DIFFRACTION99.34
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)
14.477888297133.32995997303-0.8028908609434.37688265991.968090691513.60410569205-0.375087594445-0.2270934399850.506817895762-0.615646304232.4761234875-0.326595202088-0.7696208056480.775169400915-2.627970457471.281891673390.05509416459140.007631152216321.238983914080.2350933344151.49926197664-234.257594534259.114170257284.688750012
26.22267352206-0.123828530048-0.4976466559447.451514886054.193548846899.37577703429-0.1555347181830.1578971565570.0701076896354-0.8202231874010.0932711441784-0.34646606499-0.6650286755190.8487730549320.09205191326430.4556750242510.02429881208860.02583163371290.5834504200690.1789978688490.347359649806-242.336492852257.254314908272.507197216
30.9051954788940.007268421633270.007359932019234.8399317091.707419252411.97533373468-0.288081758185-0.07650575116840.0918101294711-0.339122115080.08567881795580.11520018947-0.1508158104670.5684141586280.1857284847450.3628843882250.00384930682461-0.09042965456280.4975666931640.1629829251380.399355997277-246.026888503267.601938091285.43396984
42.50850649929-1.058537485770.5399773026325.970943256360.2043225280541.96494199913-0.218663021661-0.300420839469-0.0822547024090.4227371710450.133305918386-0.4781275428120.07297057510640.6283541705030.1217948201590.3332987352970.0492121875187-0.114343208150.6094855698430.1235151008870.351405911914-241.160852719266.325102952294.119393167
53.34494227488-0.2223720992180.6127641598515.154011755692.009715925733.77947624928-0.244886637798-0.3118824019040.05344572955770.6377703218720.234907566753-0.2986317496360.1798821527980.791708236285-0.004722150705340.364634543110.0895003042095-0.07460612882160.5623401895210.164111656670.357302778899-243.68533587258.468372146296.432340968
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 2 )BB - C1 - 2
22chain 'A' and (resid -2 through 31 )AA-2 - 311 - 34
33chain 'A' and (resid 32 through 96 )AA32 - 9635 - 80
44chain 'A' and (resid 97 through 130 )AA97 - 13081 - 114
55chain 'A' and (resid 131 through 174 )AA131 - 174115 - 158

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