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- EMDB-23264: Cryo-EM map of PDX1.2/PDX1.3 co-expression complex (Arabidopsis t... -

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Basic information

Entry
Database: EMDB / ID: EMD-23264
TitleCryo-EM map of PDX1.2/PDX1.3 co-expression complex (Arabidopsis thaliana)
Map data
Sample
  • Complex: PDX1.2/PDX1.3 heterododecamer
Function / homology
Function and homology information


response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / amino acid metabolic process / response to UV-B / response to salt stress ...response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / amino acid metabolic process / response to UV-B / response to salt stress / endomembrane system / response to oxidative stress / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsNovikova IV / Evans JE
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)66382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: ACS Chem Biol / Year: 2021
Title: Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex.
Authors: Irina V Novikova / Mowei Zhou / Chen Du / Marcelina Parra / Doo Nam Kim / Zachary L VanAernum / Jared B Shaw / Hanjo Hellmann / Vicki H Wysocki / James E Evans /
Abstract: Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is ...Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.
History
DepositionJan 8, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lb6
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lb6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23264.png

Downloads & links

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Map

FileDownload / File: emd_23264.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 303.6 Å		1.01 Å/pix.
x 300 pix.
= 303.6 Å		1.01 Å/pix.
x 300 pix.
= 303.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-1.5524131 - 5.7033124
Average (Standard dev.)0.007106256 (±0.2224535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0121.0121.012
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z303.600303.600303.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.5525.7030.007

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Supplemental data

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Sample components

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Entire : PDX1.2/PDX1.3 heterododecamer

EntireName: PDX1.2/PDX1.3 heterododecamer
Components
  • Complex: PDX1.2/PDX1.3 heterododecamer

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Supramolecule #1: PDX1.2/PDX1.3 heterododecamer

SupramoleculeName: PDX1.2/PDX1.3 heterododecamer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
Molecular weightExperimental: 445 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris, 150 mM NaCl, 4 mM. DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: at 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 510660
CTF correctionSoftware - Name: cryoSPARC (ver. 2.5) / Software - details: CTFFIND4
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 286642
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final 3D classificationNumber classes: 150
FSC plot (resolution estimation)

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