[English] 日本語
Yorodumi
- EMDB-12733: PspA helical structure in presence of lipids -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12733
TitlePspA helical structure in presence of lipids
Map datasymmetrized map from helical refinement in CryoSparc v3.1.0
Sample
  • Organelle or cellular component: PspA helical structure in presence of lipids
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.15 Å
AuthorsJunglas B / Huber ST / Heidler T / Mann D / Henning R / Clarke M / Ortiz JO / Schneider D / Sachse C
CitationJournal: Cell / Year: 2021
Title: PspA adopts an ESCRT-III-like fold and remodels bacterial membranes.
Authors: Benedikt Junglas / Stefan T Huber / Thomas Heidler / Lukas Schlösser / Daniel Mann / Raoul Hennig / Mairi Clarke / Nadja Hellmann / Dirk Schneider / Carsten Sachse /
Abstract: PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy ...PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy (cryo-EM) structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generating positive membrane curvature. Using cryo-EM, we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hotspots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
History
DepositionApr 7, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12733.png

Downloads & links

-
Map

FileDownload / File: emd_12733.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetrized map from helical refinement in CryoSparc v3.1.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 350 pix.
= 476.7 Å		1.36 Å/pix.
x 350 pix.
= 476.7 Å		1.36 Å/pix.
x 350 pix.
= 476.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.362 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115 / Movie #1: 0.115
Minimum - Maximum-0.09066657 - 0.40049982
Average (Standard dev.)0.02035544 (±0.05443281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 476.69998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3621.3621.362
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z476.700476.700476.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0910.4000.020

-
Supplemental data

-
Mask #1

Fileemd_12733_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: symmetrized and sharpened map from helical refinement in...

Fileemd_12733_additional_1.map
Annotationsymmetrized and sharpened map from helical refinement in CryoSparc v3.1.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_12733_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_12733_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PspA helical structure in presence of lipids

EntireName: PspA helical structure in presence of lipids
Components
  • Organelle or cellular component: PspA helical structure in presence of lipids
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein

-
Supramolecule #1: PspA helical structure in presence of lipids

SupramoleculeName: PspA helical structure in presence of lipids / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightExperimental: 25 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pRSET6

-
Macromolecule #1: Chloroplast membrane-associated 30 kD protein

MacromoleculeName: Chloroplast membrane-associated 30 kD protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HSSGHIDDDD KHMELFNRVG RVLKSQLTHW QQQQEAPEDL LERLLGEMEL ELIELRRALA QTIATFKSTE RQRDAQQLI AQRWYEKAQA ALDRGNEQLA REALGQRQSY QSHTEALGKS LGEQRALVEQ VRGQLQKLER KYLELKSQKN L YLARLKSA ...String:
MGHHHHHHHH HSSGHIDDDD KHMELFNRVG RVLKSQLTHW QQQQEAPEDL LERLLGEMEL ELIELRRALA QTIATFKSTE RQRDAQQLI AQRWYEKAQA ALDRGNEQLA REALGQRQSY QSHTEALGKS LGEQRALVEQ VRGQLQKLER KYLELKSQKN L YLARLKSA IAAQKIEEIA GNLDNASASS LFERIETKIL ELEAERELLN PPPSPLDKKF EQWEEQQAVE ATLAAMKARR SL PPPSS

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
10.0 mMNaH2PO4Sodium Phosphate
5.0 mg/mlE.coli polar extract lipids (SUVs)
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco easiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS TALOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1531 / Average exposure time: 3.0 sec. / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.425 Å
Applied symmetry - Helical parameters - Δ&Phi: 26.629 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 222901
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1.0)
Segment selectionNumber selected: 222901 / Software - Name: cryoSPARC (ver. 3.1.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.1.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO 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