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- PDB-7z4o: Influenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD pept... -

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Basic information

Entry
Database: PDB / ID: 7z4o
TitleInfluenza A/H7N9 polymerase core dimer with Pol II pSer5 CTD peptide mimic bound in site 2A
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')
  • RNA-directed RNA polymerase catalytic subunit
  • SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER
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 / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding / cytoplasm
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-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 6th domain / Influenza RNA polymerase PB2 C-terminal 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) / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.412 Å
AuthorsCusack, S. / Pflug, A.
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 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Polymerase acidic protein
BBB: RNA-directed RNA polymerase catalytic subunit
CCC: Polymerase basic protein 2
DDD: Polymerase acidic protein
EEE: RNA-directed RNA polymerase catalytic subunit
FFF: Polymerase basic protein 2
JJJ: SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER
KKK: SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER
UUU: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')
VVV: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,91512
Polymers340,86710
Non-polymers492
Water0
1
AAA: Polymerase acidic protein
BBB: RNA-directed RNA polymerase catalytic subunit
CCC: Polymerase basic protein 2
KKK: SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER
VVV: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 170 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)170,4586
Polymers170,4335
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24460 Å2
ΔGint-154 kcal/mol
Surface area46920 Å2
2
DDD: Polymerase acidic protein
EEE: RNA-directed RNA polymerase catalytic subunit
FFF: Polymerase basic protein 2
JJJ: SER-TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER
UUU: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 170 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)170,4586
Polymers170,4335
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24660 Å2
ΔGint-159 kcal/mol
Surface area46690 Å2
Unit cell
Length a, b, c (Å)76.474, 144.131, 336.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21DDD
32BBB
42EEE
53CCC
63FFF
74UUU
84VVV

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
111GLUGLUARGARGAAAA203 - 7164 - 517
221GLUGLUARGARGDDDD203 - 7164 - 517
332METMETARGARGBBBB1 - 6701 - 670
442METMETARGARGEEEE1 - 6701 - 670
553GLUGLUTHRTHRCCCC40 - 10640 - 106
663GLUGLUTHRTHRFFFF40 - 10640 - 106
774AAGGUUUI1 - 121 - 12
884AAGGVVVJ1 - 121 - 12

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

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Components

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Protein , 3 types, 6 molecules AAADDDBBBEEECCCFFF

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


Mass: 59383.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PA subunit residues 201-716 only i.e. excluding the endonuclease
Source: (gene. exp.) Influenza A virus / Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: M9TI86, 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: 86496.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PB2 subunit residues 1-127 only / Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1-BALF_RG43/2013(H7N9) / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A024E3M6, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 17453.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PB2 subunit residues 1-127 only / Source: (gene. exp.) Influenza A virus / Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: X5F427

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Protein/peptide / RNA chain / Non-polymers , 3 types, 6 molecules JJJKKKUUUVVV

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


Mass: 3216.893 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Four repeats of the Pol II CTD heptad with pSer5. / Source: (synth.) Homo sapiens (human)
#5: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*G)-3')


Mass: 3883.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: vRNA 5' hook / Source: (synth.) Influenza A virus
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris pH 7.0, 13 % PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.41→49.211 Å / Num. obs: 37875 / % possible obs: 73.3 % / Redundancy: 14.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.283 / Rrim(I) all: 0.306 / Net I/σ(I): 7.7
Reflection shellResolution: 3.41→3.57 Å / Rmerge(I) obs: 1.873 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1852 / CC1/2: 0.696 / Rrim(I) all: 1.946

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TU5

6tu5


Resolution: 3.412→49.211 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.847 / SU B: 39.215 / SU ML: 0.572 / Cross valid method: FREE R-VALUE / ESU R Free: 0.782
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2728 1852 4.89 %
Rwork0.2201 36023 -
all0.223 --
obs-37875 73.225 %
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: 86.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.404 Å20 Å20 Å2
2--1.569 Å2-0 Å2
3----1.166 Å2
Refinement stepCycle: LAST / Resolution: 3.412→49.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19381 524 2 0 19907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01320445
X-RAY DIFFRACTIONr_bond_other_d0.0010.01519087
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2010.011353
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.65527750
X-RAY DIFFRACTIONr_angle_other_deg1.0411.58144095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49852422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5722.3951052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81153615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.75615137
X-RAY DIFFRACTIONr_chiral_restr0.0470.22713
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024670
X-RAY DIFFRACTIONr_nbd_refined0.1820.23950
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.218265
X-RAY DIFFRACTIONr_nbtor_refined0.1560.29422
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.29924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2337
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0370.26
X-RAY DIFFRACTIONr_nbd_other0.1550.233
X-RAY DIFFRACTIONr_mcbond_it2.8119.0859721
X-RAY DIFFRACTIONr_mcbond_other2.819.0859720
X-RAY DIFFRACTIONr_mcangle_it4.8813.62112132
X-RAY DIFFRACTIONr_mcangle_other4.8813.62112133
X-RAY DIFFRACTIONr_scbond_it2.2739.34510724
X-RAY DIFFRACTIONr_scbond_other2.2739.34510724
X-RAY DIFFRACTIONr_scangle_it4.12313.93715618
X-RAY DIFFRACTIONr_scangle_other4.12313.93815619
X-RAY DIFFRACTIONr_lrange_it7.81109.51123508
X-RAY DIFFRACTIONr_lrange_other7.81109.51523509
X-RAY DIFFRACTIONr_ncsr_local_group_10.0650.0515925
X-RAY DIFFRACTIONr_ncsr_local_group_20.0460.0519560
X-RAY DIFFRACTIONr_ncsr_local_group_30.050.052006
X-RAY DIFFRACTIONr_ncsr_local_group_40.0070.051132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.064730.05008
12DDDX-RAY DIFFRACTIONLocal ncs0.064730.05008
23BBBX-RAY DIFFRACTIONLocal ncs0.046020.05009
24EEEX-RAY DIFFRACTIONLocal ncs0.046020.05009
35CCCX-RAY DIFFRACTIONLocal ncs0.050010.0501
36FFFX-RAY DIFFRACTIONLocal ncs0.050010.0501
47UUUX-RAY DIFFRACTIONLocal ncs0.006760.05013
48VVVX-RAY DIFFRACTIONLocal ncs0.006760.05013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.412-3.5010.36520.313940X-RAY DIFFRACTION26.1811
3.501-3.5970.425580.3341171X-RAY DIFFRACTION33.5609
3.597-3.7010.327680.2991398X-RAY DIFFRACTION40.9154
3.701-3.8150.327790.2871604X-RAY DIFFRACTION48.3621
3.815-3.940.265880.2691790X-RAY DIFFRACTION56.6174
3.94-4.0780.3241000.2632007X-RAY DIFFRACTION63.8485
4.078-4.2320.3071130.2542180X-RAY DIFFRACTION72.9094
4.232-4.4050.2491290.2322303X-RAY DIFFRACTION80.2111
4.405-4.6010.2791290.2212392X-RAY DIFFRACTION86.7814
4.601-4.8250.2591260.2132525X-RAY DIFFRACTION93.9738
4.825-5.0860.2391420.2032513X-RAY DIFFRACTION99.3266
5.086-5.3940.2681040.222417X-RAY DIFFRACTION100
5.394-5.7670.3331260.232255X-RAY DIFFRACTION99.8742
5.767-6.2290.311070.222125X-RAY DIFFRACTION100
6.229-6.8230.2951010.2171959X-RAY DIFFRACTION100
6.823-7.6280.258940.1821790X-RAY DIFFRACTION100
7.628-8.8070.246760.1661583X-RAY DIFFRACTION99.8195
8.807-10.7850.161720.141375X-RAY DIFFRACTION100
10.785-15.2440.214570.161080X-RAY DIFFRACTION100
15.244-49.2110.309310.299616X-RAY DIFFRACTION95.7101

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