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- PDB-6qcw: Crystal structure of influenza B polymerase initiation state with... -

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Basic information

Entry
Database: PDB / ID: 6qcw
TitleCrystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*CP*AP*UP*AP*AP*UP*AP*G)-3')
  • RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-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
KeywordsVIRAL PROTEIN / RNA dependent RNA polymerase
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
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
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsCusack, S. / Drncova, P.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Commission322586European Union
French National Research AgencyANR-18-CE11-0028 France
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structural snapshots of actively transcribing influenza polymerase.
Authors: Tomas Kouba / Petra Drncová / Stephen Cusack /
Abstract: Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter ...Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.
History
DepositionDec 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 2.0Feb 28, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_audit_support / pdbx_poly_seq_scheme / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_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.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_audit_support.country / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_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: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
M: RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*CP*AP*UP*AP*AP*UP*AP*G)-3')
R: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-3')
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,1799
Polymers278,8956
Non-polymers2853
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49850 Å2
ΔGint-310 kcal/mol
Surface area87560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.354, 200.354, 256.466
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

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


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 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 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 MRV

#4: RNA chain RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*CP*AP*UP*AP*AP*UP*AP*G)-3')


Mass: 4936.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Capped RNA 14-mer / Source: (synth.) synthetic construct (others)
#5: RNA chain RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-3')


Mass: 6525.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' end of vRNA promoter (extended) / Source: (synth.) synthetic construct (others)
#6: 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' end of vRNA promoter / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 3 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

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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: 76.91 % / Description: Marquise shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 ...Details: Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4.
PH range: 4.0-4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 81417 / % possible obs: 60.7 % / Redundancy: 8.2 % / CC1/2: 0.995 / Rrim(I) all: 0.185 / Rsym value: 0.177 / Net I/σ(I): 8.2
Reflection shellResolution: 2.88→3.12 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.677 / Rrim(I) all: 1.5 / Rsym value: 1.42 / % possible all: 60.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSG

5msg


Resolution: 2.88→50 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.915 / SU B: 38.785 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 1.756 / ESU R Free: 0.396 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23391 3942 4.8 %RANDOM
Rwork0.21453 ---
obs0.21548 77475 60.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 105.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17461 1064 15 0 18540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01418991
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716855
X-RAY DIFFRACTIONr_angle_refined_deg0.7311.63325827
X-RAY DIFFRACTIONr_angle_other_deg0.7051.67439658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96952189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09422.53921
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.358153364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.57215118
X-RAY DIFFRACTIONr_chiral_restr0.0340.22511
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0220346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023438
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.44.4458774
X-RAY DIFFRACTIONr_mcbond_other0.44.4458773
X-RAY DIFFRACTIONr_mcangle_it0.7396.66710957
X-RAY DIFFRACTIONr_mcangle_other0.7396.66710958
X-RAY DIFFRACTIONr_scbond_it0.3144.48610217
X-RAY DIFFRACTIONr_scbond_other0.3144.48610216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5936.71614871
X-RAY DIFFRACTIONr_long_range_B_refined2.13853.31321959
X-RAY DIFFRACTIONr_long_range_B_other2.13853.31221960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.882→2.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 16 -
Rwork0.33 498 -
obs--5.22 %
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)
11.412-0.39370.6130.3062-0.26330.35990.34750.9664-0.5862-0.6978-0.12040.23150.47640.1253-0.2272.0555-0.29330.02431.8781-0.29651.3127-72.57823.4011-68.3589
20.91660.0077-0.23972.89150.03691.42820.2177-0.0270.08280.4598-0.26070.0421-0.11090.16480.0430.583-0.43510.07090.3644-0.07060.2269-51.031860.4307-6.4775
31.74660.35160.13311.4224-0.68021.22450.1669-0.29870.22030.5965-0.12680.0835-0.1526-0.0317-0.04010.8868-0.42630.21710.2722-0.15680.1447-66.108457.44142.8215
40.39650.2150.51811.2596-0.19231.08260.3008-0.0274-0.03270.2035-0.2449-0.37820.2590.2947-0.05580.7407-0.34780.03640.3997-0.06680.2877-49.66538.4247-10.1518
50.80580.06280.09671.5894-1.25931.18740.04520.357-0.1531-0.1511-0.0867-0.1870.38780.04740.04160.8031-0.12870.1750.6131-0.13630.3342-52.052936.0923-39.4064
61.60520.14360.02281.3538-0.22830.21320.06050.1367-0.2942-0.0141-0.0397-0.14740.32940.0539-0.02080.9217-0.21620.08270.3748-0.0910.3194-54.750228.7795-24.905
71.28010.646-0.5731.0678-0.27920.78460.1676-0.0691-0.31090.2691-0.3079-0.33750.30250.30750.14030.8848-0.19930.02790.44130.00450.383-46.83532.2779-13.1755
80.99390.0550.1063.0759-1.11232.5290.04860.16260.34480.19370.0379-0.0631-0.1869-0.3938-0.08650.5187-0.27940.28710.3095-0.04850.3862-82.440759.1442-19.086
90.9675-1.9242-2.05094.24064.39424.5950.24150.334-0.1864-0.0419-0.51560.0774-0.1019-0.62310.27410.9263-0.2827-0.06180.88370.09840.6439-69.073556.3265-41.7636
104.1352-0.4148-1.38133.7464-1.40323.72930.27451.17750.1713-0.8647-0.00130.44170.0652-0.6978-0.27321.08-0.204-0.05421.13450.00490.3996-76.218145.7273-62.9298
111.01420.2705-0.441.1364-0.36211.4664-0.02840.63320.1209-0.41590.07670.35990.3847-0.2506-0.04830.7414-0.28970.080.62920.02610.3838-80.505749.1171-36.644
123.25560.1192-0.2352.38160.88691.59090.12431.1015-0.6704-0.52120.03030.01520.4486-0.2227-0.15461.1943-0.48420.08370.7862-0.15870.5718-97.783511.9863-23.9873
132.74610.07981.27361.00750.57132.54630.1168-0.2527-0.09770.3466-0.09510.22940.0617-0.4413-0.02170.9957-0.49730.21240.42810.02790.2059-97.251222.73672.376
143.1291-0.81090.96883.9268-1.13823.38810.0913-0.69-0.25270.5847-0.0261-0.0710.19520.0815-0.06521.0111-0.48970.10680.4738-0.00230.2651-81.254215.512517.096
1510.27428.13692.88266.86632.60851.1215-0.6091.34550.3635-0.87220.68880.2054-0.2605-0.0181-0.07981.3364-0.24840.00610.79410.08080.8207-76.704431.8728-23.194
169.0013.03791.69672.2201-0.06591.0607-0.20911.03240.17880.26430.2194-0.1741-0.13860.123-0.01030.3996-0.19890.16550.44520.06490.392-46.408577.5058-36.6587
173.2398-0.9954-0.77848.17620.41590.2060.2260.26520.06380.6808-0.2366-0.4615-0.02430.01440.01050.5144-0.08610.04790.60430.03240.4344-51.452254.2767-28.4924
1813.20935.5055-7.7415.5407-1.67955.2771-0.31340.1240.38210.56770.38580.44970.5240.1139-0.07240.6849-0.10140.09150.3860.01970.3634-63.795336.6571-23.9725
194.29081.2246-1.59491.8489-0.27390.61580.1641-0.0369-0.03210.4058-0.20560.0860.0071-0.01880.04150.6223-0.32320.15180.2177-0.00890.317-44.717163.9114-17.4483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 222
2X-RAY DIFFRACTION2A223 - 392
3X-RAY DIFFRACTION3A393 - 723
4X-RAY DIFFRACTION4B0 - 72
5X-RAY DIFFRACTION5B73 - 203
6X-RAY DIFFRACTION6B204 - 346
7X-RAY DIFFRACTION7B347 - 497
8X-RAY DIFFRACTION8B498 - 623
9X-RAY DIFFRACTION9B624 - 698
10X-RAY DIFFRACTION10B699 - 749
11X-RAY DIFFRACTION11C0 - 237
12X-RAY DIFFRACTION12C238 - 506
13X-RAY DIFFRACTION13C507 - 567
14X-RAY DIFFRACTION14C568 - 740
15X-RAY DIFFRACTION15M0 - 14
16X-RAY DIFFRACTION16R1 - 10
17X-RAY DIFFRACTION17R11 - 15
18X-RAY DIFFRACTION18R16 - 21
19X-RAY DIFFRACTION19V1 - 14

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