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- EMDB-80348: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo -

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Basic information

Entry
Database: EMDB / ID: EMD-80348
TitleArabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
Map data
Sample
  • Complex: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
    • Protein or peptide: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
KeywordsArabidopsis thaliana / trehalose-6-phosphatase synthase 8 / PLANT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsLi WJ / Lin HJ / Fan MR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
Authors: Li WJ / Lin HJ / Fan MR
History
DepositionApr 16, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80348.png

Downloads & links

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Map

FileDownload / File: emd_80348.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.)
0.75 Å/pix.
x 300 pix.
= 225. Å		0.75 Å/pix.
x 300 pix.
= 225. Å		0.75 Å/pix.
x 300 pix.
= 225. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.207
Minimum - Maximum-0.9836902 - 1.5791746
Average (Standard dev.)-0.00012856057 (±0.049674015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 225.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80348_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80348_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80348_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo

EntireName: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
Components
  • Complex: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
    • Protein or peptide: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8

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Supramolecule #1: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo

SupramoleculeName: Arabidopsis thaliana Trehalose-6-phosphate synthase 8 - apo
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8

MacromoleculeName: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: alpha,alpha-trehalose-phosphate synthase (UDP-forming)
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 102.27418 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMVSRSCANF LDLSSWDLLD FPQTPRTLPR VMTVPGIITD VDGDTTSEV TSTSGGSRER KIIVANMLPL QSKRDAETGK WCFNWDEDSL QLQLRDGFSS ETEFLYVGSL NVDIETNEQE E VSQKLLEE ...String:
MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMVSRSCANF LDLSSWDLLD FPQTPRTLPR VMTVPGIITD VDGDTTSEV TSTSGGSRER KIIVANMLPL QSKRDAETGK WCFNWDEDSL QLQLRDGFSS ETEFLYVGSL NVDIETNEQE E VSQKLLEE FNCVATFLSQ ELQEMFYLGF CKHQLWPLFH YMLPMFPDHG DRFDRRLWQA YVSANKIFSD RVMEVINPED DY VWIQDYH LMVLPTFLRK RFNRIKLGFF LHSPFPSSEI YRTLPVRDEI LRGLLNCDLI GFHTFDYARH FLSCCSRMLG LDY ESKRGH IGLDYFGRTV YIKILPVGVH MGRLESVLSL DSTAAKTKEI QEQFKGKKLV LGIDDMDIFK GISLKLIAME HLFE TYWHL KGKVVLVQIV NPARSSGKDV EEAKRETYET ARRINERYGT SDYKPIVLID RLVPRSEKTA YYAAADCCLV NAVRD GMNL VPYKYIVCRQ GTRSNKAVVD SSPRTSTLVV SEFIGCSPSL SGAIRVNPWD VDAVAEAVNS ALKMSETEKQ LRHEKH YHY ISTHDVGYWA KSFMQDLERA CRDHYSKRCW GIGFGLGFRV LSLSPSFRKL SVEHIVPVYR KTQRRAIFLD YDGTLVP ES SIVQDPSNEV VSVLKALCED PNNTVFIVSG RGRESLSNWL SPCENLGIAA EHGYFIRWKS KDEWETCYSP TDTEWRSM V EPVMRSYMEA TDGTSIEFKE SALVWHHQDA DPDFGSCQAK EMLDHLESVL ANEPVVVKRG QHIVEVKPQG VSKGLAAEK VIREMVERGE PPEMVMCIGD DRSDEDMFES ILSTVTNPEL LVQPEVFACT VGRKPSKAKY FLDDEADVLK LLRGLGDSSS SLKPSSSHT QVAFESIV

UniProtKB: Probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 8

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1004933
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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