[English] 日本語
Yorodumi
- PDB-6tu5: Influenza A/H7N9 polymerase core (apo) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tu5
TitleInfluenza A/H7N9 polymerase core (apo)
Components
  • 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


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / 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 PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / 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 / 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 acidic protein / RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.325 Å
AuthorsCusack, S. / Pflug, A.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council (ERC)322586 France
CitationJournal: Cell / Year: 2020
Title: A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase.
Authors: Joanna M Wandzik / Tomas Kouba / Manikandan Karuppasamy / Alexander Pflug / Petra Drncova / Jan Provaznik / Nayara Azevedo / Stephen Cusack /
Abstract: Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). ...Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP.
History
DepositionJan 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 27, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,2168
Polymers324,1686
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52060 Å2
ΔGint-296 kcal/mol
Surface area105910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.512, 143.173, 335.372
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
11Chains A D
22Chains B E
33Chains C F

NCS ensembles :
ID
1
2
3

-
Components

#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: N-terminal truncation deletes endonuclease
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Variant: H7N9 / 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
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB1 / Variant: H7N9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: M9TLW3, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 16203.751 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal sequence GSGSENLYFQ is linker and residual TEV cleavage site after cleavage
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB2 / Variant: H7N9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: X5F427
#4: Chemical ChemComp-MG / MAGNESIUM ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at about 9 mg/ml 0.1 M Tris pH 7.0, 8-13% PEG 8K, 0.2 M MgCl2, 0.1 M guanidine hydrochloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.325→132.024 Å / Num. obs: 50439 / % possible obs: 92.7 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.057 / Rrim(I) all: 0.199 / Net I/σ(I): 10.7
Reflection shellResolution: 3.325→3.463 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2523 / CC1/2: 0.5 / Rrim(I) all: 2.388 / % possible all: 42.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSB

4wsb


Resolution: 3.325→132.024 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 32.599 / SU ML: 0.499 / Cross valid method: FREE R-VALUE / ESU R Free: 0.617
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2675 2496 4.949 %
Rwork0.2039 --
all0.207 --
obs-50439 92.355 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.623 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2---0.485 Å20 Å2
3---0.206 Å2
Refinement stepCycle: LAST / Resolution: 3.325→132.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21142 0 2 0 21144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01321574
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720096
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.65229102
X-RAY DIFFRACTIONr_angle_other_deg1.0641.57646790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07952615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06922.341158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.956154009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6915153
X-RAY DIFFRACTIONr_chiral_restr0.0410.22825
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0223766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024489
X-RAY DIFFRACTIONr_nbd_refined0.1850.24243
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.219078
X-RAY DIFFRACTIONr_nbtor_refined0.1540.210016
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.29929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2440
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.220
X-RAY DIFFRACTIONr_nbd_other0.1790.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.22
X-RAY DIFFRACTIONr_mcbond_it5.47912.7310511
X-RAY DIFFRACTIONr_mcbond_other5.47512.7310510
X-RAY DIFFRACTIONr_mcangle_it8.9319.08513109
X-RAY DIFFRACTIONr_mcangle_other8.9319.08513110
X-RAY DIFFRACTIONr_scbond_it4.97313.06911063
X-RAY DIFFRACTIONr_scbond_other4.97313.0711064
X-RAY DIFFRACTIONr_scangle_it8.46319.41215993
X-RAY DIFFRACTIONr_scangle_other8.46319.41315994
X-RAY DIFFRACTIONr_lrange_it12.931143.06723480
X-RAY DIFFRACTIONr_lrange_other12.931143.07323481
X-RAY DIFFRACTIONr_ncsr_local_group_10.0850.0515710
X-RAY DIFFRACTIONr_ncsr_local_group_20.0810.0520781
X-RAY DIFFRACTIONr_ncsr_local_group_30.1120.053220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.325-3.4110.339440.313983X-RAY DIFFRACTION25.6943
3.411-3.5040.3131510.2922748X-RAY DIFFRACTION75.7909
3.504-3.6060.3251680.2693420X-RAY DIFFRACTION93.9267
3.606-3.7170.3081800.2683449X-RAY DIFFRACTION99.78
3.717-3.8390.3061830.2413372X-RAY DIFFRACTION99.7755
3.839-3.9730.2592040.2153271X-RAY DIFFRACTION100
3.973-4.1230.2971630.2193134X-RAY DIFFRACTION99.9697
4.123-4.2910.2611450.1983050X-RAY DIFFRACTION100
4.291-4.4820.2281380.1782970X-RAY DIFFRACTION99.7433
4.482-4.7010.2431490.1622808X-RAY DIFFRACTION99.9662
4.701-4.9550.2431380.1642662X-RAY DIFFRACTION99.8217
4.955-5.2550.31170.1872538X-RAY DIFFRACTION99.737
5.255-5.6170.311340.1912390X-RAY DIFFRACTION100
5.617-6.0670.31990.2132248X-RAY DIFFRACTION100
6.067-6.6450.3781060.2462079X-RAY DIFFRACTION100
6.645-7.4280.2461050.1981895X-RAY DIFFRACTION100
7.428-8.5740.233920.1631675X-RAY DIFFRACTION100
8.574-10.4950.21830.1581427X-RAY DIFFRACTION100
10.495-14.8130.197620.1711150X-RAY DIFFRACTION100
14.813-132.0240.294350.338674X-RAY DIFFRACTION98.7465

+
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