[English] 日本語
Yorodumi
- PDB-7ogp: Structure of the apo-state of the bacteriophage PhiKZ non-virion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ogp
TitleStructure of the apo-state of the bacteriophage PhiKZ non-virion RNA polymerase - class including clamp
Components
  • DNA-directed RNA polymerasePolymerase
  • PHIKZ055
  • PHIKZ068
  • PHIKZ074
  • PHIKZ123
KeywordsTRANSCRIPTION / RNA polymerase / PhiKZ / non-virion
Function / homologyPHIKZ123 / PHIKZ074 / PHIKZ068 / PHIKZ055
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
Authorsde Martin Garrido, N. / Lai Wan Loong, Y.T.E. / Yakunina, M. / Aylett, C.H.S.
Funding support United Kingdom, Russian Federation, 2items
OrganizationGrant numberCountry
Wellcome Trust206212/Z/17/Z United Kingdom
Russian Science Foundation19-74-10030 Russian Federation
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structure of the bacteriophage PhiKZ non-virion RNA polymerase.
Authors: Natàlia deYMartín Garrido / Mariia Orekhova / Yuen Ting Emilie Lai Wan Loong / Anna Litvinova / Kailash Ramlaul / Tatyana Artamonova / Alexei S Melnikov / Pavel Serdobintsev / Christopher ...Authors: Natàlia deYMartín Garrido / Mariia Orekhova / Yuen Ting Emilie Lai Wan Loong / Anna Litvinova / Kailash Ramlaul / Tatyana Artamonova / Alexei S Melnikov / Pavel Serdobintsev / Christopher H S Aylett / Maria Yakunina /
Abstract: Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, ...Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a 'nucleus', erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β' subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor.
History
DepositionMay 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_imaging / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12885
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHIKZ055
B: PHIKZ068
C: DNA-directed RNA polymerase
D: PHIKZ074
E: PHIKZ123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,7156
Polymers336,6495
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 5 types, 5 molecules ABCDE

#1: Protein PHIKZ055


Mass: 57976.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SDA7
#2: Protein PHIKZ068


Mass: 59419.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD94
#3: Protein DNA-directed RNA polymerase / Polymerase


Mass: 78780.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: DNA-directed RNA polymerase
#4: Protein PHIKZ074


Mass: 77513.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD88
#5: Protein PHIKZ123


Mass: 62959.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SD39

-
Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Bacteriophage PhiKZ non-virion RNA polymerase / Type: COMPLEX
Details: Expressed in E.coli from sequences obtained from the St. Petersburg lab strain of bacteriophage PhiKZ
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas virus phiKZ / Strain: St. Petersburg
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8
Details: 15 mM Tris-Cl pH 8.0, 150 mM NaCl, 0.5 mM EDTA, 2 mM MgCl2, 1 mM DTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: 1-2 s blot

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 48000 X / Nominal defocus max: 3250 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10582 / Details: TIFF movie mode
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 70 eV
Image scansSampling size: 5 µm / Width: 5096 / Height: 4092

-
Processing

EM software
IDNameVersionCategoryDetails
1EMANparticle selectionBATCHBOXER
2EPUimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
Image processingDetails: Motion correction and dose-weighting in motioncor2
CTF correctionDetails: During reconstruction in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3179799
Details: EMAN BATCHBOXER with low-pass butterworth preprocessing
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50085 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: Core conserved regions initially identified from comparison with PDB 6EDT - remainder built de novo
Atomic model buildingPDB-ID: 6EDT

6edt


Accession code: 6EDT / Source name: PDB / Type: experimental model

+
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