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- PDB-6euv: Structure of the midlink and cap-binding domains of influenza A p... -

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Basic information

Entry
Database: PDB / ID: 6euv
TitleStructure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (VX-787)
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / Influenza A polymerase / PB2 subunit / cap-binding domain / cap-binding inhibitor
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / 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
Similarity search - Domain/homology
Chem-21G / NICKEL (II) ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCusack, S. / Lethier, M.
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
DepositionOct 31, 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 / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase basic protein 2
C: Polymerase basic protein 2
F: Polymerase basic protein 2
I: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,72814
Polymers130,0974
Non-polymers2,63110
Water1,838102
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3824
Polymers32,5241
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3824
Polymers32,5241
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9823
Polymers32,5241
Non-polymers4582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9823
Polymers32,5241
Non-polymers4582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.490, 80.320, 92.320
Angle α, β, γ (deg.)89.54, 107.12, 99.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22F
13A
23I
14C
24F
15C
25I
16F
26I

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA252 - 5316 - 285
21TYRTYRCB252 - 5316 - 285
12SERSERAA252 - 5326 - 286
22SERSERFC252 - 5326 - 286
13TYRTYRAA252 - 5316 - 285
23TYRTYRID252 - 5316 - 285
14TYRTYRCB252 - 5316 - 285
24TYRTYRFC252 - 5316 - 285
15SERSERCB252 - 5336 - 287
25SERSERID252 - 5336 - 287
16TYRTYRFC252 - 5316 - 285
26TYRTYRID252 - 5316 - 285

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 32524.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cap-midlink double domain residues 247-536
Source: (gene. exp.) Influenza A virus (strain A/Victoria/3/1975 H3N2)
Gene: PB2 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P31345
#2: Chemical
ChemComp-21G / (2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid / 3-[[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid / VX787 / (2S,3S)-3-((5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl)amino)bicyclo[2.2.2]octane-2-carboxylic acid


Mass: 399.394 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H19F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were obtained by mixing protein at 16 mg per mL mixed with 2 mM VX-787 in 0.1 M MES pH6, 0.7 M sodium formate pH 6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 38468 / % possible obs: 94.8 % / Redundancy: 1.69 % / CC1/2: 0.991 / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.99
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 1.55 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.508 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EUX

6eux


Resolution: 2.7→43.35 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.915 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 3.957 / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28168 1837 4.8 %RANDOM
Rwork0.2428 ---
obs0.24469 36631 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.95 Å2-1.09 Å2
2--3.2 Å20.72 Å2
3----2.4 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8713 0 178 102 8993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199121
X-RAY DIFFRACTIONr_bond_other_d0.0020.028642
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.98812304
X-RAY DIFFRACTIONr_angle_other_deg0.953319963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37751113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8922.995414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.121151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99215105
X-RAY DIFFRACTIONr_chiral_restr0.0830.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021853
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_it3.0624.8864464
X-RAY DIFFRACTIONr_mcbond_other3.0534.8864463
X-RAY DIFFRACTIONr_mcangle_it4.937.3165573
X-RAY DIFFRACTIONr_mcangle_other4.937.3175574
X-RAY DIFFRACTIONr_scbond_it3.1055.2114657
X-RAY DIFFRACTIONr_scbond_other3.1055.2124658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0627.6776732
X-RAY DIFFRACTIONr_long_range_B_refined7.62354.7689693
X-RAY DIFFRACTIONr_long_range_B_other7.62254.7779684
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)
11A172120.04
12C172120.04
21A172860.03
22F172860.03
31A172480.04
32I172480.04
41C171560.04
42F171560.04
51C173400.04
52I173400.04
61F172140.04
62I172140.04
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 135 -
Rwork0.355 2688 -
obs--93.76 %

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