[English] 日本語
Yorodumi
- EMDB-12714: Structural basis for VIPP1 oligomerization and maintenance of thy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12714
TitleStructural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity
Map dataC18 refined map
Sample
  • Complex: VIPP1 / IM30 complex
    • Protein or peptide: Protein sll0617
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsESCRT-III / Membrane remodelling / nucleotide hydrolysis / photosynthesis / thylakoid biogenesis / stress response / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsGupta TK / Klumpe S
Funding support Germany, Japan, 7 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR 2092 EN1194/1-1 Germany
German Research Foundation (DFG)NI 390/9-2 Germany
German Research Foundation (DFG)SCHU 3364 Germany
German Research Foundation (DFG)FOR2092 Schr 617/8-2 Germany
German Research Foundation (DFG)TRR 175/C02 Germany
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06554 Japan
Japan Society for the Promotion of Science (JSPS)17H03699 Japan
CitationJournal: Cell / Year: 2021
Title: Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity.
Authors: Tilak Kumar Gupta / Sven Klumpe / Karin Gries / Steffen Heinz / Wojciech Wietrzynski / Norikazu Ohnishi / Justus Niemeyer / Benjamin Spaniol / Miroslava Schaffer / Anna Rast / Matthias ...Authors: Tilak Kumar Gupta / Sven Klumpe / Karin Gries / Steffen Heinz / Wojciech Wietrzynski / Norikazu Ohnishi / Justus Niemeyer / Benjamin Spaniol / Miroslava Schaffer / Anna Rast / Matthias Ostermeier / Mike Strauss / Jürgen M Plitzko / Wolfgang Baumeister / Till Rudack / Wataru Sakamoto / Jörg Nickelsen / Jan M Schuller / Michael Schroda / Benjamin D Engel /
Abstract: Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its ...Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-remodeling functions. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket on one end of the ring. Inside the ring's lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In vivo mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Using cryo-correlative light and electron microscopy (cryo-CLEM), we observe oligomeric VIPP1 coats encapsulating membrane tubules within the Chlamydomonas chloroplast. Our work provides a structural foundation for understanding how VIPP1 directs thylakoid biogenesis and maintenance.
History
DepositionApr 3, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7o3z
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7o3z
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12714.png

Downloads & links

-
Map

FileDownload / File: emd_12714.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC18 refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.006488559 - 0.016998151
Average (Standard dev.)0.000007978406 (±0.000991906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.0060.0170.000

-
Supplemental data

-
Mask #1

Fileemd_12714_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: C18 map before refinement

Fileemd_12714_additional_1.map
AnnotationC18 map before refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C18 half map 2

Fileemd_12714_half_map_1.map
AnnotationC18 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C18 half map 1

Fileemd_12714_half_map_2.map
AnnotationC18 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VIPP1 / IM30 complex

EntireName: VIPP1 / IM30 complex
Components
  • Complex: VIPP1 / IM30 complex
    • Protein or peptide: Protein sll0617
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: VIPP1 / IM30 complex

SupramoleculeName: VIPP1 / IM30 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

-
Macromolecule #1: Protein sll0617

MacromoleculeName: Protein sll0617 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 28.822145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ALFDRLGRVV RANLNDLVSK AEDPEKVLEQ AVIDMQEDLV QLRQAVARTI AEEKRTEQRL NQDTQEAKKW EDRAKLALTN GEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG T SSATSAFE ...String:
ALFDRLGRVV RANLNDLVSK AEDPEKVLEQ AVIDMQEDLV QLRQAVARTI AEEKRTEQRL NQDTQEAKKW EDRAKLALTN GEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG T SSATSAFE RMENKVLDME ATSQAAGELA GFGIENQFAQ LEASSGVEDE LAALKASMAG GALPGTSAAT PQLEAAPVDS SV PANNASQ DDAVIDQELD DLRRRLNNL

UniProtKB: Membrane-associated protein Vipp1

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / 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
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 18000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4whe


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial model 4whe used for comparative modelling and Rosetta to predict the missing segments
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7o3z:
Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

+
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