[English] 日本語
Yorodumi
- EMDB-18779: Structure of the non-mitochondrial citrate synthase from Ananas c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18779
TitleStructure of the non-mitochondrial citrate synthase from Ananas comosus
Map data
Sample
  • Complex: Octameric complex of non-mitochondrial/glyoxysomal citrate synthase from Ananas comosus
    • Protein or peptide: Citrate synthase
KeywordsComplex / TRANSFERASE
Function / homology
Function and homology information


citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / cytosol
Similarity search - Function
Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
Biological speciesAnanas comosus (pineapple)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsLo YK / Bohn S / Sendker FL / Schuller JM / Hochberg G
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SCHU3364/1-1 Germany
European Research Council (ERC)101040472 EVOCATIONEuropean Union
CitationJournal: bioRxiv / Year: 2024
Title: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.
Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / ...Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / Joseph W Thornton / Arvind Pillai / Gert Bange / Jan M Schuller / Georg K A Hochberg /
Abstract: Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are ...Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assemblies and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
History
DepositionOct 28, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18779.png

Downloads & links

-
Map

FileDownload / File: emd_18779.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 218. Å		1.09 Å/pix.
x 200 pix.
= 218. Å		1.09 Å/pix.
x 200 pix.
= 218. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.6513591 - 2.5567098
Average (Standard dev.)0.008459123 (±0.107392974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 218.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_18779_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18779_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Octameric complex of non-mitochondrial/glyoxysomal citrate syntha...

EntireName: Octameric complex of non-mitochondrial/glyoxysomal citrate synthase from Ananas comosus
Components
  • Complex: Octameric complex of non-mitochondrial/glyoxysomal citrate synthase from Ananas comosus
    • Protein or peptide: Citrate synthase

-
Supramolecule #1: Octameric complex of non-mitochondrial/glyoxysomal citrate syntha...

SupramoleculeName: Octameric complex of non-mitochondrial/glyoxysomal citrate synthase from Ananas comosus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ananas comosus (pineapple)

-
Macromolecule #1: Citrate synthase

MacromoleculeName: Citrate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ananas comosus (pineapple)
Molecular weightTheoretical: 57.611801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEGAFDHSAL ARARLAVLSG HLAAVSAAGG GASPLERSPV SVQEIPPPPR NLGGSLAVID GRSGKKFEFK ISDEGTVRAT DFKKITTGK NDKGLKLYDP GYLNTAPVRS SICYIDGDEG ILRYRGYPIE ELAESSSYPE VAYLLMYGNL PSKSQLADWE F AISQHSAV ...String:
MEGAFDHSAL ARARLAVLSG HLAAVSAAGG GASPLERSPV SVQEIPPPPR NLGGSLAVID GRSGKKFEFK ISDEGTVRAT DFKKITTGK NDKGLKLYDP GYLNTAPVRS SICYIDGDEG ILRYRGYPIE ELAESSSYPE VAYLLMYGNL PSKSQLADWE F AISQHSAV PQGVLDIIQG MPHDAHPMGV LVCAMSALSV FHPDANPALR GQDLYKSKQL RDKQIVRILG KVPTIAAAAY LR LAGRPPV LPSNNFSYSE NFLYMLDSLG NRSYKPNTRL ARVLDILFIL HAEHEMNCST AAARHLASSG VDVFTALAGA VGA LYGPLH GGANEAVLKM LNEIGTVENI PDFIEGVKNR KRKMSGFGHR VYKNYDPRAK VIRKLAEEVF SIVGRDPLIE VAIA LEKAA LSDEYFIKRK LYPNVDFYSG LIYRAMGFPT EFFPVLFAIP RMAGYLAHWR ESLDDPDTKI MRPQQVYTGV WLRHY TPLQ ERTVSNDEDK LGQVAVSNAT RRRLAGSRIL EHHHHHH

UniProtKB: Citrate synthase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108304
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlvh1.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