[English] 日本語
Yorodumi
- EMDB-13827: Single Particle Cryo-EM structure of photosynthetic A8B8 glyceral... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13827
TitleSingle Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.
Map dataA8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer
Sample
  • Complex: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach) / spinach (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsMarotta R / Fermani S / Sparla F / Trost P / Del Giudice A
Funding support France, 1 items
OrganizationGrant numberCountry
Grenoble Instruct-ERIC Center (ISBG)PID 1829 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Unravelling the regulation pathway of photosynthetic AB-GAPDH.
Authors: Roberto Marotta / Alessandra Del Giudice / Libero Gurrieri / Silvia Fanti / Paolo Swuec / Luciano Galantini / Giuseppe Falini / Paolo Trost / Simona Fermani / Francesca Sparla /
Abstract: Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic ...Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme in the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant isoform is formed by AB heterotetramers and the least abundant by A homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of its B subunits. Reversible inhibition of AB-GAPDH occurs via the oxidation of a cysteine pair located in the CTE and the substitution of NADP(H) with NAD(H) in the cofactor-binding site. These combined conditions lead to a change in the oligomerization state and enzyme inhibition. SEC-SAXS and single-particle cryo-EM analysis were applied to reveal the structural basis of this regulatory mechanism. Both approaches revealed that spinach (AB)-GAPDH oligomers with n = 1, 2, 4 and 5 co-exist in a dynamic system. B subunits mediate the contacts between adjacent tetramers in AB and AB oligomers. The CTE of each B subunit penetrates into the active site of a B subunit of the adjacent tetramer, which in turn moves its CTE in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H), by removing NADP(H) from A subunits, allows the entrance of the CTE into the active site of the B subunit, hence stabilizing inhibited oligomers.
History
DepositionNov 2, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13827.png

Downloads & links

-
Map

FileDownload / File: emd_13827.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 300 pix.
= 363. Å		1.21 Å/pix.
x 300 pix.
= 363. Å		1.21 Å/pix.
x 300 pix.
= 363. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125
Minimum - Maximum-0.017907947 - 0.05063842
Average (Standard dev.)0.0002327111 (±0.0026156849)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 363.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer -...

Fileemd_13827_half_map_1.map
AnnotationA8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: A8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer -...

Fileemd_13827_half_map_2.map
AnnotationA8B8 photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) hexadecamer - minor oligomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...

EntireName: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
Components
  • Complex: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

-
Supramolecule #1: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (...

SupramoleculeName: A8B8 glyceraldehyde-3-phospahte dehydrogenase hetero-hexdecamer (minor conformer)complexed with NAD.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Spinacia oleracea (spinach)

-
Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: spinach (spinach)
Molecular weightTheoretical: 39.403957 KDa
SequenceString: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVVNDSGGVK SATHLLKYDS ILGTFKADVK IIDNETFSID GKPIKVVSNR DPLKLPWAE LGIDIVIEGT GVFVDGPGAG KHIQAGAKKV IITAPAKGSD IPTYVVGVNE KDYGHDVANI ISNASCTTNC L APFVKVLD ...String:
KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVVNDSGGVK SATHLLKYDS ILGTFKADVK IIDNETFSID GKPIKVVSNR DPLKLPWAE LGIDIVIEGT GVFVDGPGAG KHIQAGAKKV IITAPAKGSD IPTYVVGVNE KDYGHDVANI ISNASCTTNC L APFVKVLD EELGIVKGTM TTTHSYTGDQ RLLDASHRDL RRARAAALNI VPTSTGAAKA VSLVLPQLKG KLNGIALRVP TP NVSVVDL VVNIEKVGVT AEDVNNAFRK AAAGPLKGVL DVCDIPLVSV DFRCSDFSST IDSSLTMVMG GDMVKVVAWY DNE WGYSQR VVDLADLVAN KWPGLEGSVA SGDPLEDFCK DNPADEECKL YE

-
Macromolecule #2: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: spinach (spinach)
Molecular weightTheoretical: 36.256391 KDa
SequenceString: KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVINDTGGVK QASHLLKYDS ILGTFDADVK TAGDSAISVD GKVIKVVSDR NPVNLPWGD MGIDLVIEGT GVFVDRDGAG KHLQAGAKKV LITAPGKGDI PTYVVGVNEE GYTHADTIIS NASCTTNCLA P FVKVLDQK ...String:
KLKVAINGFG RIGRNFLRCW HGRKDSPLDV VVINDTGGVK QASHLLKYDS ILGTFDADVK TAGDSAISVD GKVIKVVSDR NPVNLPWGD MGIDLVIEGT GVFVDRDGAG KHLQAGAKKV LITAPGKGDI PTYVVGVNEE GYTHADTIIS NASCTTNCLA P FVKVLDQK FGIIKGTMTT THSYTGDQRL LDASHRDLRR ARAACLNIVP TSTGAAKAVA LVLPNLKGKL NGIALRVPTP NV SVVDLVV QVSKKTFAEE VNAAFRESAD NELKGILSVC DEPLVSIDFR CTDVSSTIDS SLTMVMGDDM VKVIAWYDNE WGY SQRVVD LADIVANKWQ A

-
Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 16 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10768
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2pkq

Output model

PDB-7q56:
Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

+
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