[English] 日本語
Yorodumi
- EMDB-15490: 200 A SynPspA rod after incubation with ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15490
Title200 A SynPspA rod after incubation with ATP
Map data
Sample
  • Complex: Phage shock protein A (PspA)
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsNucleotide binding / Helical assembly / ESCRT-III fold / Membrane remodeling / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJunglas B / Hudina E / Schoennenbeck P / Ritter I / Santiago-Schuebel B / Huesgen P / Sachse C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.
Authors: Benedikt Junglas / Esther Hudina / Philipp Schönnenbeck / Ilona Ritter / Anja Heddier / Beatrix Santiago-Schübel / Pitter F Huesgen / Dirk Schneider / Carsten Sachse /
Abstract: Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) ...Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) has been identified as a member of the ESCRT-III superfamily, and PspA homo-oligomerizes to form rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms tubular assemblies of varying diameters. Using electron cryo-electron microscopy, we determined 61 Synechocystis PspA structures and observed in molecular detail how the structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed and changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III members.
History
DepositionJul 31, 2022-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15490.png

Downloads & links

-
Map

FileDownload / File: emd_15490.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 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: 0.12
Minimum - Maximum-0.3749976 - 0.855278
Average (Standard dev.)0.0018597047 (±0.01890098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15490_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local filtered map

Fileemd_15490_additional_1.map
AnnotationLocal filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15490_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15490_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Phage shock protein A (PspA)

EntireName: Phage shock protein A (PspA)
Components
  • Complex: Phage shock protein A (PspA)
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Phage shock protein A (PspA)

SupramoleculeName: Phage shock protein A (PspA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 97.5 kDa/nm

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

MacromoleculeName: Chloroplast membrane-associated 30 kD protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 28.097758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSSAALEVLF QGPMELFNRV GRVLKSQLTH WQQQQEAPED LLERLLGEME LELIELRRAL AQTIATFKST ERQRDAQQL IAQRWYEKAQ AALDRGNEQL AREALGQRQS YQSHTEALGK SLGEQRALVE QVRGQLQKLE RKYLELKSQK N LYLARLKS ...String:
MGSSHHHHHH SSSAALEVLF QGPMELFNRV GRVLKSQLTH WQQQQEAPED LLERLLGEME LELIELRRAL AQTIATFKST ERQRDAQQL IAQRWYEKAQ AALDRGNEQL AREALGQRQS YQSHTEALGK SLGEQRALVE QVRGQLQKLE RKYLELKSQK N LYLARLKS AIAAQKIEEI AGNLDNASAS SLFERIETKI LELEAERELL NPPPSPLDKK FEQWEEQQAV EATLAAMKAR RS LPPPSS

UniProtKB: Chloroplast membrane-associated 30 kD protein

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.75 Å
Applied symmetry - Helical parameters - Δ&Phi: 34.4 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64979
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7abk

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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