[English] 日本語
Yorodumi
- EMDB-20648: CryoEM Structure of Pyocin R2 - postcontracted - baseplate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20648
TitleCryoEM Structure of Pyocin R2 - postcontracted - baseplate
Map data
SamplePyocin R2 - Postcontracted:
Sheath PA0622 / Glue PA0627 / Tri1a PA0618 / Tri2 PA0619 / Sheath Initiator PA0617
Function / homology
Function and homology information


Tail protein I / Baseplate protein J-like / IraD/Gp25-like / Phage Tail Protein X-like / Baseplate assembly protein J, predicted / Tail sheath protein, C-terminal domain / Tail sheath protein, subtilisin-like domain / LysM domain superfamily
Probable bacteriophage protein / Probable bacteriophage protein / Probable bacteriophage protein / Uncharacterized protein / Probable bacteriophage protein
Biological speciesPseudomonas aeruginosa PAO1 (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGe P / Avaylon J / Scholl D / Shneider MM / Browning C / Buth SA / Plattner M / Ding K / Leiman PG / Miller JF / Zhou ZH
Funding support United States, Switzerland, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
Swiss National Science Foundation31003A_146284 Switzerland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI085318 United States
National Science Foundation (NSF, United States)XSEDE MCB140140 United States
CitationJournal: Nature / Year: 2020
Title: Action of a minimal contractile bactericidal nanomachine.
Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff ...Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff F Miller / Z Hong Zhou /
Abstract: R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded ...R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionAug 27, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseApr 15, 2020-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u5k
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20648.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 420 pix.
= 437.22 Å
1.04 Å/pix.
x 420 pix.
= 437.22 Å
1.04 Å/pix.
x 420 pix.
= 437.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.107300244 - 0.18900001
Average (Standard dev.)0.00001367018 (±0.010422632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 437.22 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z437.220437.220437.220
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ460460460
MAP C/R/S123
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-0.1070.1890.000

-
Supplemental data

-
Sample components

+
Entire Pyocin R2 - Postcontracted

EntireName: Pyocin R2 - Postcontracted / Number of components: 6

+
Component #1: protein, Pyocin R2 - Postcontracted

ProteinName: Pyocin R2 - Postcontracted / Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa PAO1 (bacteria)

+
Component #2: protein, Sheath PA0622

ProteinName: Sheath PA0622 / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 41.247332 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

+
Component #3: protein, Glue PA0627

ProteinName: Glue PA0627 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 7.486475 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

+
Component #4: protein, Tri1a PA0618

ProteinName: Tri1a PA0618 / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 31.986117 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

+
Component #5: protein, Tri2 PA0619

ProteinName: Tri2 PA0619 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 20.013682 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

+
Component #6: protein, Sheath Initiator PA0617

ProteinName: Sheath Initiator PA0617 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 11.862759 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2160.0 nm / Energy filter: GIF Quantum LS / Energy window: -10-10 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (80.0 - 81.0 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 7331

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 15581
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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