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- PDB-6evj: Crystal structure of bat influenza A/H17N10 polymerase with viral... -

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Basic information

Entry
Database: PDB / ID: 6evj
TitleCrystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and capped RNA primer
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')
  • RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
  • RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / Influenza virus / RNA-dependent RNA polymerase / capped RNA primer
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / 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-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / 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 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsPflug, A. / Cusack, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.
Authors: Pflug, A. / Gaudon, S. / Resa-Infante, P. / Lethier, M. / Reich, S. / Schulze, W.M. / Cusack, S.
History
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Author supporting evidence / Database references / Source and taxonomy
Category: citation / entity_src_gen / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization
Revision 1.2Feb 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Feb 28, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / 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 / _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_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
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2
N: RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')
R: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
S: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
M: RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')
U: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)559,06712
Polymers559,06712
Non-polymers00
Water00
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
R: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
M: RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)279,5336
Polymers279,5336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2
N: RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')
S: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
U: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)279,5336
Polymers279,5336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.460, 286.170, 171.930
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F
14R
24S
15U
25V

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA0 - 71414 - 728
21SERSERGLYGLYDD0 - 71414 - 728
12METMETGLYGLYBB1 - 75710 - 766
22METMETGLYGLYEE1 - 75710 - 766
13GLYGLYILEILECC0 - 7439 - 752
23GLYGLYILEILEFF0 - 7439 - 752
14UUUURH1 - 131 - 13
24UUUUSI1 - 131 - 13
15AAGGUK1 - 151 - 15
25AAGGVL1 - 151 - 15

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Polymerase acidic protein


Mass: 85490.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag and linker C-terminal linker and TEV cleavage site
Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM92
#2: Protein RNA-directed RNA polymerase catalytic subunit


Mass: 87936.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker and TEV cleavage site
Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2


Mass: 91027.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker, STREP tag and TEV cleavage site
Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))
Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90

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RNA chain , 3 types, 6 molecules NMRSUV

#4: RNA chain RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')


Mass: 4246.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic capped RNA 12-mer / Source: (synth.) synthetic construct (others)
#5: RNA chain RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')


Mass: 5584.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Viral RNA promoter 3 primed end / Source: (synth.) Influenza A virus
#6: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')


Mass: 5248.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Viral RNA promoter 5 primed end / Source: (synth.) Influenza A virus

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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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine pH 9.0, 17% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 81025 / % possible obs: 99.8 % / Redundancy: 3.87 % / CC1/2: 0.998 / Rrim(I) all: 0.137 / Rsym value: 0.118 / Net I/σ(I): 8.28
Reflection shellResolution: 3.9→4 Å / Redundancy: 3.87 % / Mean I/σ(I) obs: 0.93 / CC1/2: 0.539 / Rrim(I) all: 1.44 / Rsym value: 1.24 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSB

4wsb


Resolution: 3.9→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 51.563 / SU ML: 0.622 / Cross valid method: THROUGHOUT / ESU R Free: 0.673 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 4018 5 %RANDOM
Rwork0.20668 ---
obs0.20857 77007 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 181.471 Å2
Baniso -1Baniso -2Baniso -3
1--12.7 Å20 Å22.43 Å2
2--5.24 Å20 Å2
3---7.13 Å2
Refinement stepCycle: 1 / Resolution: 3.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35378 1339 0 0 36717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01937549
X-RAY DIFFRACTIONr_bond_other_d0.0010.0234374
X-RAY DIFFRACTIONr_angle_refined_deg0.9631.92950944
X-RAY DIFFRACTIONr_angle_other_deg0.8562.99979927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07554398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31724.0621701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.533156720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.19115276
X-RAY DIFFRACTIONr_chiral_restr0.0550.25606
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02140408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027658
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_it3.69418.34617634
X-RAY DIFFRACTIONr_mcbond_other3.69318.34617633
X-RAY DIFFRACTIONr_mcangle_it6.32827.51322018
X-RAY DIFFRACTIONr_mcangle_other6.32827.51322019
X-RAY DIFFRACTIONr_scbond_it3.14118.81119915
X-RAY DIFFRACTIONr_scbond_other3.1418.81119914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.64428.07328927
X-RAY DIFFRACTIONr_long_range_B_refined9.51343237
X-RAY DIFFRACTIONr_long_range_B_other9.51343238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A450100.02
12D450100.02
21B470680.02
22E470680.02
31C455760.03
32F455760.03
41R19060.01
42S19060.01
51U28500
52V28500
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 288 -
Rwork0.381 5599 -
obs--98.56 %

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