[English] 日本語
Yorodumi
- PDB-9f37: Replication-like initiation state of influenza polymerase with GT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f37
TitleReplication-like initiation state of influenza polymerase with GTP and CTP at respectively the -1 and +1 positions (strain A/little yellow-shouldered bat/Guatemala/060/2010/H17N10)
Components
  • 3' end of the vRNA promoter
  • 5' end of the vRNA promoter
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase
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 / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase ...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 / 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 / DNA-templated transcription / GTP binding / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
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 / : ...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 / 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
CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.905 Å
AuthorsCusack, S. / Drncova, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0028 France
CitationJournal: Biorxiv / Year: 2024
Title: High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit
Authors: Cusack, S. / Drncova, P. / Krischuns, T. / Naffakh, N.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
R: 3' end of the vRNA promoter
V: 5' end of the vRNA promoter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,28315
Polymers276,2285
Non-polymers2,05510
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.937, 119.005, 251.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein Polymerase acidic protein


Mass: 85490.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag and C-terminal linker and TEV cleavage site
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010/H17N10
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 and C-terminal linker and TEV cleavage site
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010/H17N10
Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2


Mass: 91027.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker and C-terminal linker and double STREP tag
Source: (gene. exp.) Influenza A virus
Strain: A/little yellow-shouldered bat/Guatemala/060/2010/H17N10
Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90

-
RNA chain , 2 types, 2 molecules RV

#4: RNA chain 3' end of the vRNA promoter


Mass: 6525.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus
#5: RNA chain 5' end of the vRNA promoter


Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus

-
Non-polymers , 6 types, 710 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 % / Description: long prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5 mg/ml polymerase with 5.1 mg/ml (19.5 microM) with 1.14 x molar excess of each RNA (v5' 1-16, v3' 1-18+3 and 15-mer capped primer, see Figure 1a) mixed in 1:1 ratio of 100 mM amino acids, ...Details: 5 mg/ml polymerase with 5.1 mg/ml (19.5 microM) with 1.14 x molar excess of each RNA (v5' 1-16, v3' 1-18+3 and 15-mer capped primer, see Figure 1a) mixed in 1:1 ratio of 100 mM amino acids, 100 mM Tris/Bicine pH8.5, 8% ethylene glycol (v/v), 4% PEG 8000 (w/v) by hanging drop at room temperature. Soaking was performed with 5 mM GTP, 5 mM CTP and 5 mM MgCl2 for 5h.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.905→86.6 Å / Num. obs: 151625 / % possible obs: 71.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Net I/σ(I): 13.3
Reflection shellResolution: 1.91→2.11 Å / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 283 / CC1/2: 0.708 / Rrim(I) all: 1.04

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.905→86.566 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.464 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2315 7590 5.006 %
Rwork0.1891 144035 -
all0.191 --
obs-151625 71.224 %
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: 49.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.165 Å2-0 Å20 Å2
2--0.223 Å2-0 Å2
3----0.058 Å2
Refinement stepCycle: LAST / Resolution: 1.905→86.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17411 639 126 700 18876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01218747
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617529
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.8425478
X-RAY DIFFRACTIONr_angle_other_deg0.4951.77240421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87652201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.4995138
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.189525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.745103320
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.19610845
X-RAY DIFFRACTIONr_chiral_restr0.070.22836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024357
X-RAY DIFFRACTIONr_nbd_refined0.2190.24092
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.216793
X-RAY DIFFRACTIONr_nbtor_refined0.1840.29107
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.29938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2926
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.24
X-RAY DIFFRACTIONr_nbd_other0.1510.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.29
X-RAY DIFFRACTIONr_mcbond_it3.6235.0038774
X-RAY DIFFRACTIONr_mcbond_other3.6235.0038774
X-RAY DIFFRACTIONr_mcangle_it5.5098.96510985
X-RAY DIFFRACTIONr_mcangle_other5.5088.96510986
X-RAY DIFFRACTIONr_scbond_it3.8765.3259973
X-RAY DIFFRACTIONr_scbond_other3.8765.3259973
X-RAY DIFFRACTIONr_scangle_it6.0939.61914493
X-RAY DIFFRACTIONr_scangle_other6.0939.61914494
X-RAY DIFFRACTIONr_lrange_it8.16945.82221642
X-RAY DIFFRACTIONr_lrange_other8.17145.78821501
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
1.905-1.9550.419150.3352680.339155790.9240.9281.81650.334
1.955-2.0080.312620.30411130.305151890.9380.9487.73590.302
2.008-2.0660.2961440.27530330.276148290.9450.95221.42420.268
2.066-2.130.2662330.25144310.252143780.9560.95932.43840.245
2.13-2.20.2763820.24466830.246139340.950.96250.70330.232
2.2-2.2770.2645030.23798030.238134970.9550.96376.35770.221
2.277-2.3630.2756510.238119360.24130030.950.96396.80070.221
2.363-2.4590.2756480.224119160.227125860.950.96899.82520.202
2.459-2.5680.2565860.207114290.209120160.9610.97499.99170.186
2.568-2.6940.2455700.19109660.192115440.9650.97899.93070.17
2.694-2.8390.2455250.186104840.189110090.9630.9791000.168
2.839-3.0110.2394910.1998960.192103890.9630.97899.98080.173
3.011-3.2190.2344760.19293180.19497970.9650.97999.96940.179
3.219-3.4760.2394720.20186830.20391600.9680.97999.94540.19
3.476-3.8080.2414200.19380240.19584470.9680.98199.96450.185
3.808-4.2560.1953890.16472710.16676600.9780.9851000.16
4.256-4.9120.2033680.14364140.14667820.9770.9881000.145
4.912-6.0110.2342850.1855300.18358160.9710.98499.98280.182
6.011-8.4810.2062230.17943310.1845600.9780.98499.86840.185
8.481-86.5660.1931470.18225060.18226650.9740.97399.54970.209

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more