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- PDB-25sw: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - T6P -

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Basic information

Entry
Database: PDB / ID: 25sw
TitleArabidopsis thaliana Trehalose-6-phosphate synthase 8 - T6P
ComponentsProbable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
KeywordsPLANT PROTEIN / Arabidopsis thaliana / Trehalose-6-phosphate synthase 8
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / trehalose biosynthetic process / catalytic activity / chloroplast / cytoplasm
Similarity search - Function
Trehalose-phosphatase / Trehalose-phosphatase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLi, W.J. / Lin, H.J. / Fan, M.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - T6P
Authors: Li, W.J. / Lin, H.J. / Fan, M.R.
History
DepositionApr 16, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
B: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,3934
Polymers204,5482
Non-polymers8452
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8 / Trehalose-6-phosphate synthase 8 / AtTPS8


Mass: 102274.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPS8, TPS2, TPSC, At1g70290, F17O7.18 / Production host: Homo sapiens (human)
References: UniProt: Q0WUI9, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-6-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 422.277 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OPO/3O/3=O]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - T6P
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1004933 / Symmetry type: POINT
RefinementHighest resolution: 2.35 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028212
ELECTRON MICROSCOPYf_angle_d0.4511104
ELECTRON MICROSCOPYf_dihedral_angle_d9.2261112
ELECTRON MICROSCOPYf_chiral_restr0.0411210
ELECTRON MICROSCOPYf_plane_restr0.0031410

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