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- PDB-7z42: Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound ... -

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Basic information

Entry
Database: PDB / ID: 7z42
TitleInfluenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B
Components
  • DNA-directed RNA polymerase II subunit RPB1
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')
  • RNA-directed RNA polymerase catalytic subunit
KeywordsRNA BINDING PROTEIN / Influenza RNA-dependent RNA polymerase / transcription / cap-snatching / Pol II CTD
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 / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression ...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 / 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 / nucleotide binding / RNA-directed RNA polymerase activity / 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 polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...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 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
RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.418 Å
AuthorsCusack, S. / Drncova, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0028 France
CitationJournal: Plos Pathog. / Year: 2022
Title: Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD.
Authors: Krischuns, T. / Isel, C. / Drncova, P. / Lukarska, M. / Pflug, A. / Paisant, S. / Navratil, V. / Cusack, S. / Naffakh, N.
History
DepositionMar 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Y: DNA-directed RNA polymerase II subunit RPB1
G: DNA-directed RNA polymerase II subunit RPB1
H: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')
X: DNA-directed RNA polymerase II subunit RPB1
I: DNA-directed RNA polymerase II subunit RPB1
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)547,04112
Polymers547,04112
Non-polymers00
Water3,711206
1
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
Y: DNA-directed RNA polymerase II subunit RPB1
G: DNA-directed RNA polymerase II subunit RPB1
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)273,5206
Polymers273,5206
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41240 Å2
ΔGint-241 kcal/mol
Surface area88630 Å2
MethodPISA
2
D: Polymerase acidic protein
E: RNA-directed RNA polymerase catalytic subunit
F: Polymerase basic protein 2
H: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')
X: DNA-directed RNA polymerase II subunit RPB1
I: DNA-directed RNA polymerase II subunit RPB1


Theoretical massNumber of molelcules
Total (without water)273,5206
Polymers273,5206
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40490 Å2
ΔGint-247 kcal/mol
Surface area87860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.930, 202.269, 135.733
Angle α, β, γ (deg.)90.000, 110.538, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
32B
42E
53C
63F
74H
84V
95I
105G

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLUGLUAA0 - 72214 - 736
211SERSERGLUGLUDD0 - 72214 - 736
322METMETSERSERBB1 - 75410 - 763
422METMETSERSEREE1 - 75410 - 763
533METMETLYSLYSCC1 - 74010 - 749
633METMETLYSLYSFF1 - 74010 - 749
744AAAAHI1 - 131 - 13
844AAAAVL1 - 131 - 13
955TYRTYRTHRTHRIK29 - 461 - 18
1055TYRTYRTHRTHRGH29 - 461 - 18

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Polymerase acidic protein


Mass: 85822.781 Da / Num. of mol.: 2 / Mutation: K135A
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.: 2
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.: 2
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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Protein/peptide / RNA chain / Non-polymers , 3 types, 212 molecules YGXIHV

#4: Protein/peptide
DNA-directed RNA polymerase II subunit RPB1


Mass: 3216.893 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Four repeat Pol II CTD peptide mimic with pSer5 / Source: (synth.) Homo sapiens (human)
References: DNA-directed RNA polymerase, RNA-directed RNA polymerase
#5: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3')


Mass: 4212.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5' vRNA hook / Source: (synth.) Influenza B virus
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 ...Details: FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.25422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25422 Å / Relative weight: 1
ReflectionResolution: 2.418→127.106 Å / Num. obs: 154519 / % possible obs: 61.4 % / Redundancy: 3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.136 / Net I/σ(I): 7.7
Reflection shellResolution: 2.42→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7573 / CC1/2: 0.63 / Rrim(I) all: 0.769 / % possible all: 64

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FMZ

5fmz


Resolution: 2.418→127.106 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.223 / SU B: 9.426 / SU ML: 0.215 / Average fsc free: 0.8891 / Average fsc work: 0.9001 / Cross valid method: FREE R-VALUE / ESU R: 2.182 / ESU R Free: 0.367
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2567 7573 4.901 %
Rwork0.2233 146946 -
all0.225 --
obs-154519 61.415 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å2-0 Å20.054 Å2
2--0.129 Å2-0 Å2
3----0.105 Å2
Refinement stepCycle: LAST / Resolution: 2.418→127.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35189 532 0 206 35927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01336486
X-RAY DIFFRACTIONr_bond_other_d0.0010.01534904
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2180.012530
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6549296
X-RAY DIFFRACTIONr_angle_other_deg1.0561.58380628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25854414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52822.5631838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.749156744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46315232
X-RAY DIFFRACTIONr_chiral_restr0.0460.24790
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0240414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028216
X-RAY DIFFRACTIONr_nbd_refined0.1720.26317
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.231919
X-RAY DIFFRACTIONr_nbtor_refined0.150.217077
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.218175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2627
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.215
X-RAY DIFFRACTIONr_nbd_other0.1760.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.23
X-RAY DIFFRACTIONr_mcbond_it1.3035.77217698
X-RAY DIFFRACTIONr_mcbond_other1.3035.77117697
X-RAY DIFFRACTIONr_mcangle_it2.3288.64822098
X-RAY DIFFRACTIONr_mcangle_other2.3288.64922099
X-RAY DIFFRACTIONr_scbond_it1.035.80418788
X-RAY DIFFRACTIONr_scbond_other1.035.80418788
X-RAY DIFFRACTIONr_scangle_it1.8888.63227198
X-RAY DIFFRACTIONr_scangle_other1.8888.63227199
X-RAY DIFFRACTIONr_lrange_it4.20467.19641299
X-RAY DIFFRACTIONr_lrange_other4.20467.241294
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0522260
X-RAY DIFFRACTIONr_ncsr_local_group_20.0640.0523038
X-RAY DIFFRACTIONr_ncsr_local_group_30.0850.0521321
X-RAY DIFFRACTIONr_ncsr_local_group_40.0160.051226
X-RAY DIFFRACTIONr_ncsr_local_group_50.0880.05421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.073810.05008
12DX-RAY DIFFRACTIONLocal ncs0.073810.05008
23BX-RAY DIFFRACTIONLocal ncs0.063510.05009
24EX-RAY DIFFRACTIONLocal ncs0.063510.05009
35CX-RAY DIFFRACTIONLocal ncs0.085370.05008
36FX-RAY DIFFRACTIONLocal ncs0.085370.05008
47HX-RAY DIFFRACTIONLocal ncs0.015610.05014
48VX-RAY DIFFRACTIONLocal ncs0.015610.05014
59IX-RAY DIFFRACTIONLocal ncs0.088150.05009
510GX-RAY DIFFRACTIONLocal ncs0.088150.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.418-2.4810.257100.3272250.324185260.7940.8381.26850.327
2.481-2.5490.345670.31112260.313180730.8290.8597.15430.311
2.549-2.6220.3461390.31726350.319176560.8220.84615.71140.317
2.622-2.7030.3011860.30939130.309170540.8390.83724.03540.309
2.703-2.7920.3352720.30350620.305165900.8380.84732.15190.303
2.792-2.890.3363250.29469680.296160250.8340.84845.51010.294
2.89-2.9990.3164810.28393350.284154560.8310.85563.50930.283
2.999-3.1210.2936530.271121070.272149230.8610.86385.50560.271
3.121-3.260.3046590.266128860.268142800.8560.87294.85290.266
3.26-3.4190.2876340.25125880.252136670.870.88796.7440.25
3.419-3.6030.2916190.237119020.239130030.8890.90896.29320.237
3.603-3.8220.245940.218112040.219122910.9190.92795.98890.218
3.822-4.0850.2315060.205105660.206115820.9270.93595.59660.205
4.085-4.4120.2185000.18797210.188107560.9360.94395.0260.187
4.412-4.8330.2134500.17988990.18199110.940.94894.32950.179
4.833-5.4020.2254510.19479810.19689950.9340.94193.7410.194
5.402-6.2360.2773460.22170520.22379510.9130.92493.04490.221
6.236-7.6330.2492810.21358500.21567180.9170.92691.26230.213
7.633-10.7760.2082530.16844330.1752080.9460.95789.9770.168
10.776-127.1060.2681470.25323930.25429330.9060.89186.60080.253

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