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- PDB-5d98: Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212 -

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Basic information

Entry
Database: PDB / ID: 5d98
TitleInfluenza C Virus RNA-dependent RNA Polymerase - Space group P43212
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsTRANSFERASE/RNA / RNA-dependent RNA polymerase / Influenza / Influenza C virus / Negative-strand virus / transferase-RNA complex
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 / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / 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 / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / 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-dependent RNA polymerase subunit PB2 / 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 / 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
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.9 Å
AuthorsHengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust092931/Z/10/Z United Kingdom
Medical Research Council (United Kingdom)MR/K000241/1 United Kingdom
Medical Research Council (United Kingdom)G1000099 United Kingdom
Medical Research Council (United Kingdom)G1100138 United Kingdom
Wellcome Trust075491/Z/04 United Kingdom
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the RNA-dependent RNA polymerase from influenza C virus.
Authors: Hengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,38510
Polymers514,2886
Non-polymers974
Water00
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,1935
Polymers257,1443
Non-polymers492
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,1935
Polymers257,1443
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.660, 185.660, 598.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA4 - 7084 - 708
21THRTHRTHRTHRDD4 - 7084 - 708
12METMETSERSERBB1 - 7531 - 753
22METMETSERSEREE1 - 7531 - 753
13METMETLYSLYSCC1 - 7711 - 771
23METMETLYSLYSFF1 - 7711 - 771

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.685073, -0.720346, -0.108516), (0.724762, -0.688997, -0.001829), (-0.07345, -0.079901, 0.994093)-158.578766, 56.801472, 67.556961

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Components

#1: Protein Polymerase acidic protein / Polymerase 3 / RNA-directed RNA polymerase subunit P2


Mass: 82025.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Gene: PA, P3 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP5
#2: Protein RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86145.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Gene: PB1 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP4, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 88972.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966)
Gene: PB2 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.21 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ...Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium l-tartrate, 0.2 M sodium oxamate), 0.1 M MES/imidazole) in a 2:1 protein:precipitant ratio.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9763
SYNCHROTRONDiamond I0321.035
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 2, 2015
DECTRIS PILATUS 6M2PIXELApr 14, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.0351
ReflectionResolution: 3.9→100.57 Å / Num. obs: 95267 / % possible obs: 98.8 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.2
Reflection shellResolution: 3.9→4 Å / Redundancy: 20.6 % / Rmerge(I) obs: 3.685 / Mean I/σ(I) obs: 1.3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
PHENIXphasing
SHELXphasing
Aimlessdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.9→50.01 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 80.769 / SU ML: 0.987 / Cross valid method: THROUGHOUT / ESU R Free: 0.805 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32572 4770 5 %RANDOM
Rwork0.28578 ---
obs0.2878 90335 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 205.572 Å2
Baniso -1Baniso -2Baniso -3
1-9.73 Å2-0 Å2-0 Å2
2--9.73 Å2-0 Å2
3----19.47 Å2
Refinement stepCycle: 1 / Resolution: 3.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34716 0 4 0 34720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01935362
X-RAY DIFFRACTIONr_bond_other_d0.0040.0234482
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9747528
X-RAY DIFFRACTIONr_angle_other_deg1.679379634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66354310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49324.1851596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.506156842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.46115242
X-RAY DIFFRACTIONr_chiral_restr0.0520.25220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02139190
X-RAY DIFFRACTIONr_gen_planes_other0.0030.027876
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_it9.6320.32117306
X-RAY DIFFRACTIONr_mcbond_other9.62920.32117305
X-RAY DIFFRACTIONr_mcangle_it15.74630.47321594
X-RAY DIFFRACTIONr_mcangle_other15.74530.47421595
X-RAY DIFFRACTIONr_scbond_it9.07720.99518056
X-RAY DIFFRACTIONr_scbond_other9.07720.99518057
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.14131.23325935
X-RAY DIFFRACTIONr_long_range_B_refined21.75643100
X-RAY DIFFRACTIONr_long_range_B_other21.75643100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A662810.47
2B674210.16
3C723214.44
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.54 355 -
Rwork0.51 6402 -
obs--96.85 %

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