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- PDB-25sy: Triticum aestivum Trehalose-6-phosphate synthase 5 - T6P -

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Basic information

Entry
Database: PDB / ID: 25sy
TitleTriticum aestivum Trehalose-6-phosphate synthase 5 - T6P
Componentsalpha,alpha-trehalose-phosphate synthase (UDP-forming)
KeywordsPLANT PROTEIN / Triticum aestivum / Trehalose-6-phosphate synthase 5
Function / homology
Function and homology information


trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / cytosol
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
alpha,alpha-trehalose-phosphate synthase (UDP-forming)
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.23 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: Triticum aestivum Trehalose-6-phosphate synthase 5 - T6P
Authors: Li, W.J. / Lin, H.J.
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: alpha,alpha-trehalose-phosphate synthase (UDP-forming)
B: alpha,alpha-trehalose-phosphate synthase (UDP-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,7844
Polymers211,9392
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 alpha,alpha-trehalose-phosphate synthase (UDP-forming) / Trehalose 6-phosphate phosphatase


Mass: 105969.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of author provided organism is not available during the biocuration, replaced by corresponding Uniprot reference temporarily.
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Homo sapiens (human)
References: UniProt: A0A453KSC9, 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: Triticum aestivum Trehalose-6-phosphate synthase 5 - T6P
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Triticum aestivum (bread wheat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 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: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2078834 / Symmetry type: POINT
RefinementHighest resolution: 2.23 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048354
ELECTRON MICROSCOPYf_angle_d0.611300
ELECTRON MICROSCOPYf_dihedral_angle_d10.2581140
ELECTRON MICROSCOPYf_chiral_restr0.0441218
ELECTRON MICROSCOPYf_plane_restr0.0051446

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