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- PDB-6cfp: CRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA ... -

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Basic information

Entry
Database: PDB / ID: 6cfp
TitleCRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA A VIRUS, WILSON-SMITH/1933 (H1N1) BOUND TO FRAGMENT HIT BSI-70565 1-{1-[4-FLUOROPHENYL)METHYL]-2-METHYL-1H-IMIDAZOL-4-YL}ETHAN-1-ONE
ComponentsUbiquitin-like protein SMT3,Polymerase acidic protein
KeywordsVIRAL PROTEIN / INFLUENZA / H1N1 / FRAGMENT-BASED DRUG DISCOVERY / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


RNA polymerase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring ...RNA polymerase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / negative regulation of viral transcription / SUMOylation of chromatin organization proteins / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein sumoylation / condensed nuclear chromosome / protein tag activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-templated transcription / host cell nucleus / RNA binding / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-EZS / Polymerase acidic protein / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA A VIRUS, WILSON-SMITH/1933 (H1N1) BOUND TO FRAGMENT HIT BSI-70565 1-{1-[4-FLUOROPHENYL)METHYL]-2-METHYL-1H-IMIDAZOL-4-YL}ETHAN-1-ONE
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Davies, D.R. / Abendroth, J. / Lorimer, D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4553
Polymers64,1441
Non-polymers3102
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.820, 68.820, 397.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-995-

HOH

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Components

#1: Protein Ubiquitin-like protein SMT3,Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 64144.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Influenza A virus
Strain: ATCC 204508 / S288c, A/Wilson-Smith/1933 H1N1 / Gene: SMT3, YDR510W, D9719.15, PA / Production host: Escherichia coli (E. coli)
References: UniProt: Q12306, UniProt: P15659, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-EZS / 1-{1-[(4-fluorophenyl)methyl]-2-methyl-1H-imidazol-4-yl}ethan-1-one


Mass: 232.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MOLECULAR DIMENSIONS MORPHEUS SCREEN D10: 10% PEG 8000, 20% ETHYLENE GLYCOL; 20MM OF EACH 1, 6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL, 1,3-PROPANEDIOL; 100MM ...Details: MOLECULAR DIMENSIONS MORPHEUS SCREEN D10: 10% PEG 8000, 20% ETHYLENE GLYCOL; 20MM OF EACH 1, 6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4- BUTANEDIOL, 1,3-PROPANEDIOL; 100MM TRIS/BICINE PH 8.5; INVAA.07057.A.D15. AT 20.0 MG/ML, OVERNIGHT SOAK WITH 7 MM BSI70565, DIRECT CRYO; tray 297881d10, puck WXU6-7
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 1, 2018
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 21829 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.38 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.87
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 4.72 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13_2998: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUJ

4iuj


Resolution: 2.45→41.13 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.231 1946 8.92 %
Rwork0.179 --
obs-21825 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 21 104 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073232
X-RAY DIFFRACTIONf_angle_d0.8124374
X-RAY DIFFRACTIONf_dihedral_angle_d12.921958
X-RAY DIFFRACTIONf_chiral_restr0.045489
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.51120.26251350.20051348X-RAY DIFFRACTION100
2.5112-2.57910.29891410.19631369X-RAY DIFFRACTION100
2.5791-2.6550.27481610.19731377X-RAY DIFFRACTION100
2.655-2.74070.25941430.19161357X-RAY DIFFRACTION100
2.7407-2.83860.2791570.20131368X-RAY DIFFRACTION100
2.8386-2.95220.2681210.18871386X-RAY DIFFRACTION100
2.9522-3.08650.26661240.18681406X-RAY DIFFRACTION100
3.0865-3.24920.22821370.19611408X-RAY DIFFRACTION100
3.2492-3.45270.24781270.1821425X-RAY DIFFRACTION100
3.4527-3.71910.22511340.17571415X-RAY DIFFRACTION100
3.7191-4.09310.23721440.17051425X-RAY DIFFRACTION100
4.0931-4.68460.19081330.14121462X-RAY DIFFRACTION100
4.6846-5.89940.19741380.17441495X-RAY DIFFRACTION100
5.8994-41.13560.2221510.19361638X-RAY DIFFRACTION100
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)
11.08190.10850.08593.1596-1.30933.7254-0.11270.0124-0.1499-0.23750.05970.04940.3607-0.23080.04570.42550.09310.09270.27570.03810.2655-17.5367-36.839253.6649
20.6185-0.61141.26126.2477-0.99322.8649-0.4113-0.5113-0.1250.46840.38030.74090.0435-0.66250.02090.43490.12280.07830.4370.09360.349-24.4496-40.233469.2971
31.332-0.1421-0.39052.689-2.65284.7217-0.120.0798-0.0077-0.0921-0.2167-0.50140.240.51330.37490.43640.15640.09130.37310.02740.4024-7.6132-33.640352.5419
41.1148-0.34920.31122.0119-0.67022.5869-0.00850.13740.2155-0.20.061-0.0203-0.3738-0.2223-0.03790.42610.13770.09010.36370.07580.3242-19.4785-22.867249.0074
56.47514.1361-5.35756.2249-2.98185.5013-0.3235-0.29470.0354-0.4759-0.2645-0.8002-0.27981.00080.6090.515-0.03990.05470.58910.24330.61944.3296-17.754839.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 330 )
2X-RAY DIFFRACTION2chain 'A' and (resid 331 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 415 )
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 652 )
5X-RAY DIFFRACTION5chain 'A' and (resid 653 through 713 )

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