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- PDB-7lm4: The crystal structure of the I38T mutant PA Endonuclease (2009/H1... -

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Basic information

Entry
Database: PDB / ID: 7lm4
TitleThe crystal structure of the I38T mutant PA Endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
: / Hexa Vinylpyrrolidone K15 / Chem-Y5V / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Jayaraman, S. / Rankovic, Z. / White, S.W.
Citation
Journal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5998
Polymers23,1361
Non-polymers1,4627
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-43 kcal/mol
Surface area9610 Å2
Unit cell
Length a, b, c (Å)89.216, 89.216, 131.779
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 42 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-Y5V / 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 395.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.57 Å / Num. obs: 11436 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 50.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 19
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1101 / CC1/2: 0.691 / Rpim(I) all: 0.442 / Rrim(I) all: 1.134 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.35→39.41 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 536 4.69 %
Rwork0.2073 10898 -
obs0.2091 11434 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.41 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 87 35 1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311588
X-RAY DIFFRACTIONf_angle_d0.61372147
X-RAY DIFFRACTIONf_chiral_restr0.043223
X-RAY DIFFRACTIONf_plane_restr0.004270
X-RAY DIFFRACTIONf_dihedral_angle_d19.5987579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.590.33161400.26712651X-RAY DIFFRACTION99.96
2.59-2.960.27811120.26452699X-RAY DIFFRACTION99.96
2.96-3.730.2551380.21672703X-RAY DIFFRACTION99.96
3.73-39.410.2261460.18212845X-RAY DIFFRACTION99.8
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)
18.317000826662.25137829572-4.783926155066.404093613240.5675976555823.391134265460.290414124884-0.64845328734-0.4142703645672.013733365840.683875567352-0.610837329419-0.1645681408520.479827830509-1.028696449570.7737997268880.0109099391823-0.1258803597720.6311043020170.0946359998620.634862013292-21.1660559826-28.7736122373-1.08923662583
26.09760017622-1.363041903511.832174579889.465839196294.124550416452.740141558420.181386835751-0.426631172713-0.4041511417631.134313202770.0484676377888-1.362012413160.9659561044361.2981357812-0.2628811728620.6937991706860.0509982231879-0.06653995418190.8705691839280.2926385780740.669165551025-17.5495579189-39.2341549753-4.14454175555
35.775951152591.737445351135.149418471484.938850361313.784984750647.63584377728-0.175467506994-0.1879276226130.1931462174440.208132198776-0.0193292830320.1412157971150.478391626465-0.05842250349580.1231725246710.376859360167-0.06324173564570.03859136987340.429891148930.1794759037390.47555845403-22.8639712386-36.0584550383-14.0914332174
42.90173468946-0.669720347939-0.8371469422587.44178192784-0.3977237084142.59376953811-0.3608139915230.318308124674-0.295504707022-0.4569744454190.179466841075-0.1631976439070.3249761648840.5073186031610.1616894474710.414230306866-0.04932636486840.1740849759790.5516677576120.1264198613220.409201558037-21.1797197269-48.4116099077-22.040596278
58.75419525533-3.729368937981.663432103692.13396303323-0.4519695655087.283492805940.4927743801340.1123672753090.284094494489-0.8950292510780.236659963496-0.431597393094-0.126144132192-0.709411455442-0.8078910516270.660072820691-0.2140913546360.179584194491.298681966110.1233182691490.683971203317-10.650408723-35.6851185164-26.8620292187
63.09955391526-1.17055411396-0.1932392986818.030340088534.573264741528.29865954259-0.07617006812680.4837116622930.415135744417-0.874505053596-0.0142417946676-0.868376676306-0.498787965574-0.0718502910970.0914280193130.473440328696-0.1935932338370.1042642585120.6637360245190.2063462429130.449557004587-20.6714798697-36.6218828308-29.2396678343
70.821648840533-1.960110661380.08336721292214.255699959332.261717881344.6113093802-0.223473991405-0.1490316637130.468686128761-0.205559342896-0.1035392771640.0184097595098-0.6668802116770.5018507539860.1709464266870.413032969473-0.220349607904-0.06244381452930.5617377904370.3091432456650.455550040522-23.2002594389-25.0871545458-16.7742931168
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -6 through 10 )-6 - 101 - 17
22chain 'A' and (resid 11 through 31 )11 - 3118 - 38
33chain 'A' and (resid 32 through 50 )32 - 5039 - 57
44chain 'A' and (resid 51 through 126 )51 - 12658 - 114
55chain 'A' and (resid 127 through 138 )127 - 138115 - 126
66chain 'A' and (resid 139 through 164 )139 - 164127 - 152
77chain 'A' and (resid 165 through 195 )165 - 195153 - 183

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