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- PDB-7z43: Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound ... -

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Basic information

Entry
Database: PDB / ID: 7z43
TitleInfluenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*CP*CP*UP*GP*CP*U)-3')
  • RNA (5'-R(P*AP*AP*UP*CP*A)-3')
  • RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')
  • RNA-directed RNA polymerase catalytic subunit
  • SER-TYR-SER-PRO-THR-SEP-PRO
KeywordsRNA BINDING PROTEIN / Influenza RNA-dependent RNA polymerase / transcription / cap-snatching / Pol II CTD
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / 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 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Chem-IC5 / PHOSPHATE ION / RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.123 Å
AuthorsCusack, S. / Drncova, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0028 France
CitationJournal: Plos Pathog. / Year: 2022
Title: Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.
Authors: Krischuns, T. / Isel, C. / Drncova, P. / Lukarska, M. / Pflug, A. / Paisant, S. / Navratil, V. / Cusack, S. / Naffakh, N.
History
DepositionMar 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Polymerase acidic protein
BBB: RNA-directed RNA polymerase catalytic subunit
CCC: Polymerase basic protein 2
RRR: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*CP*CP*UP*GP*CP*U)-3')
VVV: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')
MaM: RNA (5'-R(P*AP*AP*UP*CP*A)-3')
XXX: SER-TYR-SER-PRO-THR-SEP-PRO
YYY: SER-TYR-SER-PRO-THR-SEP-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,11410
Polymers283,5608
Non-polymers5532
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.819, 200.819, 257.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules AAABBBCCC

#1: Protein Polymerase acidic protein


Mass: 85822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag C-terminal linker and TEV site / Source: (gene. exp.) Influenza B virus / Gene: PA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds
#2: Protein RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86207.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker and TEV protease site
Source: (gene. exp.) Influenza B virus / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 90844.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal STREP-tag and TEV protease site
Source: (gene. exp.) Influenza B virus / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3

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RNA chain , 3 types, 3 molecules RRRVVVMaM

#4: RNA chain RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*CP*CP*UP*GP*CP*U)-3')


Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vRNA template / Source: (synth.) Influenza B virus
#5: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')


Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' vRNA hook / Source: (synth.) Influenza B virus
#6: RNA chain RNA (5'-R(P*AP*AP*UP*CP*A)-3')


Mass: 4110.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Capped RNA primer / Source: (synth.) Homo sapiens (human)

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Protein/peptide , 1 types, 2 molecules XXXYYY

#7: Protein/peptide SER-TYR-SER-PRO-THR-SEP-PRO


Mass: 3216.893 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Four repeats of Pol II CTD heptad with pSer5 / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-IC5 / [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.33 Å3/Da / Density % sol: 76.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 200 mM di-ammonium phosphate, and 100 mM sodium acetate at pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.12→76.972 Å / Num. obs: 77848 / % possible obs: 73.1 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.149 / Net I/σ(I): 8
Reflection shellResolution: 3.12→3.32 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3951 / CC1/2: 0.536 / Rrim(I) all: 1.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSG

5msg


Resolution: 3.123→76.972 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.879 / SU B: 25.401 / SU ML: 0.388 / Cross valid method: FREE R-VALUE / ESU R: 17.94 / ESU R Free: 0.48
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2723 3951 5.075 %
Rwork0.2396 73897 -
all0.241 --
obs-77848 73.077 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 108.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.025 Å2-0.012 Å2-0 Å2
2---0.025 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.123→76.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17684 745 34 1 18464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01318890
X-RAY DIFFRACTIONr_bond_other_d0.0010.01517781
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2310.011193
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.65425635
X-RAY DIFFRACTIONr_angle_other_deg0.9931.58441091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.79552216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6822.492927
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.123102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411153388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.19615119
X-RAY DIFFRACTIONr_chiral_restr0.0480.22521
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0220580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024228
X-RAY DIFFRACTIONr_nbd_refined0.1590.23440
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1460.216267
X-RAY DIFFRACTIONr_nbtor_refined0.1510.28652
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.28966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0570.211
X-RAY DIFFRACTIONr_nbd_other0.1220.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.24
X-RAY DIFFRACTIONr_mcbond_it2.16511.5998885
X-RAY DIFFRACTIONr_mcbond_other2.16511.5998884
X-RAY DIFFRACTIONr_mcangle_it3.78517.39411094
X-RAY DIFFRACTIONr_mcangle_other3.78517.39411095
X-RAY DIFFRACTIONr_scbond_it1.72811.6810005
X-RAY DIFFRACTIONr_scbond_other1.72811.6810002
X-RAY DIFFRACTIONr_scangle_it3.20817.43214541
X-RAY DIFFRACTIONr_scangle_other3.20817.43114536
X-RAY DIFFRACTIONr_lrange_it6.33213821409
X-RAY DIFFRACTIONr_lrange_other6.332138.00421410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.123-3.2040.398540.3691087X-RAY DIFFRACTION14.5815
3.204-3.2920.3311130.3631901X-RAY DIFFRACTION26.4895
3.292-3.3870.3281320.3572456X-RAY DIFFRACTION35.1439
3.387-3.4910.3461430.3523064X-RAY DIFFRACTION44.5355
3.491-3.6060.3542010.343530X-RAY DIFFRACTION53.3839
3.606-3.7320.3182010.3224178X-RAY DIFFRACTION64.826
3.732-3.8730.3342910.315350X-RAY DIFFRACTION86.8113
3.873-4.0310.3553160.2985908X-RAY DIFFRACTION99.061
4.031-4.210.33160.2735680X-RAY DIFFRACTION99.4856
4.21-4.4160.2793090.2525386X-RAY DIFFRACTION98.5124
4.416-4.6540.2882940.2415119X-RAY DIFFRACTION98.3645
4.654-4.9360.2512300.2244803X-RAY DIFFRACTION97.4066
4.936-5.2770.272210.2254461X-RAY DIFFRACTION94.6624
5.277-5.6990.2712200.2274206X-RAY DIFFRACTION96.849
5.699-6.2430.262130.2163987X-RAY DIFFRACTION99.5969
6.243-6.9780.2762110.2113606X-RAY DIFFRACTION99.2202
6.978-8.0560.1861650.183187X-RAY DIFFRACTION98.5303
8.056-9.8610.1811490.1562664X-RAY DIFFRACTION96.6667
9.861-13.9230.1841050.1592089X-RAY DIFFRACTION96.482
13.923-76.9720.373670.3021235X-RAY DIFFRACTION97.0194

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