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- EMDB-23263: Cryo-EM map of pyridoxal 5'-phosphate synthase-like subunit PDX1.... -

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Basic information

Entry
Database: EMDB / ID: EMD-23263
TitleCryo-EM map of pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis thaliana)
Map data
Sample
  • Complex: PDX1.2 dodecamer
Function / homology
Function and homology information


pyridoxal phosphate biosynthetic process / protein heterodimerization activity / 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-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: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lb5
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lb5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23263.png

Downloads & links

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Map

FileDownload / File: emd_23263.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.)
0.76 Å/pix.
x 400 pix.
= 303.6 Å		0.76 Å/pix.
x 400 pix.
= 303.6 Å		0.76 Å/pix.
x 400 pix.
= 303.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.759 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49 / Movie #1: 0.8
Minimum - Maximum-1.1045548 - 3.1610682
Average (Standard dev.)0.008142249 (±0.119651094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 303.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7590.7590.759
M x/y/z400400400
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/NS400400400
D min/max/mean-1.1053.1610.008

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Supplemental data

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Sample components

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Entire : PDX1.2 dodecamer

EntireName: PDX1.2 dodecamer
Components
  • Complex: PDX1.2 dodecamer

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Supramolecule #1: PDX1.2 dodecamer

SupramoleculeName: PDX1.2 dodecamer / type: complex / ID: 1 / Parent: 0
Details: Native conditions. Buffer: 50 mM Tris, pH7.5, 150 mM NaCl, 4 mM DTT.
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
Molecular weightExperimental: 449 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
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 787982
CTF correctionSoftware - Name: cryoSPARC (ver. 2.5) / Software - details: CTFFIND
Startup modelType of model: OTHER / Details: The initial model was generated ab initio.
Final reconstructionApplied 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: 265224
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final 3D classificationNumber classes: 150 / Software - Name: cryoSPARC (ver. 2.5)
FSC plot (resolution estimation)

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