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- PDB-5m3h: Bat influenza A/H17N10 polymerase bound to four heptad repeats of... -

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Basic information

Entry
Database: PDB / ID: 5m3h
TitleBat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
  • RNA 5'-pAGUAGUAACAAGAGGG
  • RNA-directed RNA polymerase catalytic subunit
  • TYR-SER-PRO-THR-SEP-PRO
KeywordsTRANSFERASE / influenza RNA-dependent RNA polymerase / vRNA promoter / Pol II serine 5 phosphorylated CTD peptide
Function / homology
Function and homology information


microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / cap snatching / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / virion component / promoter-specific chromatin binding / DNA-templated transcription termination / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / host cell cytoplasm / transcription by RNA polymerase II / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / ubiquitin protein ligase binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / 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 helical domain / Influenza RNA polymerase PB2 CAP binding 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. / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein / DNA-directed RNA polymerase II subunit RPB1
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLukarska, M. / Pflug, A. / Cusack, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nature / Year: 2017
Title: Structural basis of an essential interaction between influenza polymerase and Pol II CTD.
Authors: Lukarska, M. / Fournier, G. / Pflug, A. / Resa-Infante, P. / Reich, S. / Naffakh, N. / Cusack, S.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Dec 27, 2017Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.details / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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
R: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')
V: RNA 5'-pAGUAGUAACAAGAGGG
X: TYR-SER-PRO-THR-SEP-PRO
Y: TYR-SER-PRO-THR-SEP-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,10223
Polymers279,6137
Non-polymers1,49016
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46510 Å2
ΔGint-401 kcal/mol
Surface area90130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.490, 147.520, 88.480
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Polymerase acidic protein


Mass: 84241.633 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 A virus / 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.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) Influenza A virus / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2


Mass: 90168.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker, C-terminal linker and STREP tag and TEV site
Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90

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RNA chain , 2 types, 2 molecules RV

#4: 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.: 1 / Source method: obtained synthetically / Details: 3 prime end of influenza vRNA promoter / Source: (synth.) Influenza A virus
#5: RNA chain RNA 5'-pAGUAGUAACAAGAGGG


Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5 prime end of influenza vRNA promoter / Source: (synth.) Influenza A virus

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Protein/peptide , 1 types, 2 molecules XY

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


Mass: 3216.893 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to 4 heptad repeats of serine 5 phosphorylated Pol II CTD
Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS

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Non-polymers , 3 types, 266 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Bat influenza polymerase at 10 mgs per ml in 50 mM HEPES NaOH, 500 mM NaCl, 5% (v/v) glycerol, 2 mM TCEP at pH 7.5 with 1:1 ratio of vRNA promoter and CTD peptide mixed with 0.7-1.5 M ...Details: Bat influenza polymerase at 10 mgs per ml in 50 mM HEPES NaOH, 500 mM NaCl, 5% (v/v) glycerol, 2 mM TCEP at pH 7.5 with 1:1 ratio of vRNA promoter and CTD peptide mixed with 0.7-1.5 M sodium/potassium phosphate at pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 117997 / % possible obs: 99.6 % / Redundancy: 5.84 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.45
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.21 / CC1/2: 0.562 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSB

4wsb


Resolution: 2.5→49.528 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.73
RfactorNum. reflection% reflection
Rfree0.2449 5756 4.88 %
Rwork0.21 --
obs0.2118 117997 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17603 600 76 250 18529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218683
X-RAY DIFFRACTIONf_angle_d0.52925349
X-RAY DIFFRACTIONf_dihedral_angle_d15.37611312
X-RAY DIFFRACTIONf_chiral_restr0.0392810
X-RAY DIFFRACTIONf_plane_restr0.0033145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.52830.35711780.3263798X-RAY DIFFRACTION99
2.5283-2.55810.36981750.32873708X-RAY DIFFRACTION100
2.5581-2.58930.34971970.31723754X-RAY DIFFRACTION100
2.5893-2.6220.33982170.30443642X-RAY DIFFRACTION99
2.622-2.65650.33932100.29763705X-RAY DIFFRACTION99
2.6565-2.69290.31072060.28513742X-RAY DIFFRACTION99
2.6929-2.73140.30581950.27463649X-RAY DIFFRACTION99
2.7314-2.77220.2951850.26543739X-RAY DIFFRACTION100
2.7722-2.81550.34521900.26653736X-RAY DIFFRACTION100
2.8155-2.86160.29981610.2623792X-RAY DIFFRACTION100
2.8616-2.9110.31521890.26273742X-RAY DIFFRACTION100
2.911-2.96390.31932280.27133684X-RAY DIFFRACTION100
2.9639-3.02090.28411920.26053739X-RAY DIFFRACTION100
3.0209-3.08260.29451770.24533729X-RAY DIFFRACTION100
3.0826-3.14960.27591910.24453738X-RAY DIFFRACTION99
3.1496-3.22280.28441850.23613698X-RAY DIFFRACTION100
3.2228-3.30340.23591920.22563763X-RAY DIFFRACTION99
3.3034-3.39270.30791730.21823739X-RAY DIFFRACTION99
3.3927-3.49250.27652240.21553736X-RAY DIFFRACTION100
3.4925-3.60520.26311690.20873740X-RAY DIFFRACTION100
3.6052-3.7340.25762020.20533756X-RAY DIFFRACTION100
3.734-3.88350.23371860.19443754X-RAY DIFFRACTION100
3.8835-4.06010.23841910.18423748X-RAY DIFFRACTION100
4.0601-4.27410.22261570.17593779X-RAY DIFFRACTION99
4.2741-4.54170.19451880.1663749X-RAY DIFFRACTION100
4.5417-4.89210.18431960.1583772X-RAY DIFFRACTION100
4.8921-5.38390.20791890.17623760X-RAY DIFFRACTION100
5.3839-6.16170.22221990.20283775X-RAY DIFFRACTION100
6.1617-7.75820.22021760.20233791X-RAY DIFFRACTION100
7.7582-49.53810.19542380.18963784X-RAY DIFFRACTION99

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