[English] 日本語
Yorodumi
- PDB-6nm5: F-pilus/MS2 Maturation protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nm5
TitleF-pilus/MS2 Maturation protein complex
Components
  • Maturation protein
  • Type IV conjugative transfer system pilin TraA
KeywordsPROTEIN BINDING / MS2 maturation protein / F-pilus / adsorption complex
Function / homology
Function and homology information


viral genome circularization / : / virion attachment to host cell pilus / membrane => GO:0016020 / virion component / RNA binding / extracellular region
Similarity search - Function
TraA / TraA / Assembly protein / Phage maturation protein
Similarity search - Domain/homology
Chem-KSV / Type IV conjugative transfer system pilin TraA / Maturation protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage MS2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsMeng, R. / Chang, J. / Zhang, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U24GM1167 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the adsorption of a single-stranded RNA bacteriophage.
Authors: Ran Meng / Mengqiu Jiang / Zhicheng Cui / Jeng-Yih Chang / Kailu Yang / Joanita Jakana / Xinzhe Yu / Zhao Wang / Bo Hu / Junjie Zhang /
Abstract: Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of ...Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9397
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9397
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: Type IV conjugative transfer system pilin TraA
1B: Type IV conjugative transfer system pilin TraA
1C: Type IV conjugative transfer system pilin TraA
1D: Type IV conjugative transfer system pilin TraA
1E: Type IV conjugative transfer system pilin TraA
1F: Type IV conjugative transfer system pilin TraA
1G: Type IV conjugative transfer system pilin TraA
1H: Type IV conjugative transfer system pilin TraA
1I: Type IV conjugative transfer system pilin TraA
1J: Type IV conjugative transfer system pilin TraA
1K: Type IV conjugative transfer system pilin TraA
1L: Type IV conjugative transfer system pilin TraA
1M: Type IV conjugative transfer system pilin TraA
1N: Type IV conjugative transfer system pilin TraA
1O: Type IV conjugative transfer system pilin TraA
2A: Type IV conjugative transfer system pilin TraA
2B: Type IV conjugative transfer system pilin TraA
2C: Type IV conjugative transfer system pilin TraA
2D: Type IV conjugative transfer system pilin TraA
2E: Type IV conjugative transfer system pilin TraA
2F: Type IV conjugative transfer system pilin TraA
2G: Type IV conjugative transfer system pilin TraA
2H: Type IV conjugative transfer system pilin TraA
2I: Type IV conjugative transfer system pilin TraA
2J: Type IV conjugative transfer system pilin TraA
2K: Type IV conjugative transfer system pilin TraA
2L: Type IV conjugative transfer system pilin TraA
2M: Type IV conjugative transfer system pilin TraA
2N: Type IV conjugative transfer system pilin TraA
2O: Type IV conjugative transfer system pilin TraA
3A: Type IV conjugative transfer system pilin TraA
3B: Type IV conjugative transfer system pilin TraA
3C: Type IV conjugative transfer system pilin TraA
3D: Type IV conjugative transfer system pilin TraA
3E: Type IV conjugative transfer system pilin TraA
3F: Type IV conjugative transfer system pilin TraA
3G: Type IV conjugative transfer system pilin TraA
3H: Type IV conjugative transfer system pilin TraA
3I: Type IV conjugative transfer system pilin TraA
3J: Type IV conjugative transfer system pilin TraA
3K: Type IV conjugative transfer system pilin TraA
3L: Type IV conjugative transfer system pilin TraA
3M: Type IV conjugative transfer system pilin TraA
3N: Type IV conjugative transfer system pilin TraA
3O: Type IV conjugative transfer system pilin TraA
4A: Type IV conjugative transfer system pilin TraA
4B: Type IV conjugative transfer system pilin TraA
4C: Type IV conjugative transfer system pilin TraA
4D: Type IV conjugative transfer system pilin TraA
4E: Type IV conjugative transfer system pilin TraA
4F: Type IV conjugative transfer system pilin TraA
4G: Type IV conjugative transfer system pilin TraA
4H: Type IV conjugative transfer system pilin TraA
4I: Type IV conjugative transfer system pilin TraA
4J: Type IV conjugative transfer system pilin TraA
4K: Type IV conjugative transfer system pilin TraA
4L: Type IV conjugative transfer system pilin TraA
4M: Type IV conjugative transfer system pilin TraA
4N: Type IV conjugative transfer system pilin TraA
4O: Type IV conjugative transfer system pilin TraA
5A: Type IV conjugative transfer system pilin TraA
5B: Type IV conjugative transfer system pilin TraA
5C: Type IV conjugative transfer system pilin TraA
5D: Type IV conjugative transfer system pilin TraA
5E: Type IV conjugative transfer system pilin TraA
5F: Type IV conjugative transfer system pilin TraA
5G: Type IV conjugative transfer system pilin TraA
5H: Type IV conjugative transfer system pilin TraA
5I: Type IV conjugative transfer system pilin TraA
5J: Type IV conjugative transfer system pilin TraA
5K: Type IV conjugative transfer system pilin TraA
5L: Type IV conjugative transfer system pilin TraA
5M: Type IV conjugative transfer system pilin TraA
5N: Type IV conjugative transfer system pilin TraA
5O: Type IV conjugative transfer system pilin TraA
M: Maturation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,381146
Polymers556,37276
Non-polymers14,00970
Water00
1


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

-
Components

#1: Protein ...
Type IV conjugative transfer system pilin TraA


Mass: 6831.216 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1Y2ZDR2
#2: Protein Maturation protein / MP / Assembly protein / A protein


Mass: 44030.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage MS2 (virus) / References: UniProt: P03610
#3: Chemical...
ChemComp-KSV / (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate


Mass: 200.127 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C5H13O6P

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1F-pilus/MS2 maturation protein complexCOMPLEXF-pilus/MS2 Maturation protein complex#1-#20NATURAL
2Enterobacteria phage MS2 maturation proteinCOMPLEX#21NATURAL
3F-pilusCOMPLEX#11NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Enterobacteria phage MS2 (virus)329852
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 8 sec. / Electron dose: 37 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 30 eV

-
Processing

EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.13model refinement
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168989 / Symmetry type: POINT

+
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