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- EMDB-68132: Cryo-EM structure of TLP-0 -

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Basic information

Entry
Database: EMDB / ID: EMD-68132
TitleCryo-EM structure of TLP-0
Map dataCryo-EM structure of TLP-0
Sample
  • Complex: TLP-0
KeywordsGlycofibril / CARBOHYDRATE
Biological speciesalgae metagenome (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan N / Li Z / Wang T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92478205 China
CitationJournal: Cell Chem Biol / Year: 2026
Title: CryoSeek identification of glycofibrils with diverse compositions and structural assemblies.
Authors: Zhangqiang Li / Tongtong Wang / Yitong Sun / Kui Xu / Wenze Huang / Qiangfeng Cliff Zhang / Chuangye Yan / Mingxu Hu / Nieng Yan /
Abstract: CryoSeek is a research strategy that employs cryo-electron microscopy (cryo-EM) to discover bio-entities from accessible sources, supplemented with AI-facilitated data processing and bioinformatic ...CryoSeek is a research strategy that employs cryo-electron microscopy (cryo-EM) to discover bio-entities from accessible sources, supplemented with AI-facilitated data processing and bioinformatic analyses. Here we report CryoSeek-based characterization of more glycofibrils isolated from the Tsinghua Lotus Pond (TLP), named TLP-0/2/3/4b/IPT, with resolutions ranging from 3.0-3.5 Å. These glycofibrils, all covered with dense glycoshells, have various mass percentiles of the central protein components. TLP-0 has no protein at all, TLP-2 and TLP-4b each only have a linear chain of di- or tetra-peptide repeats, respectively; the central stem of TLP-3 is a trimer of linear tripeptide repeats, and IPT (immunoglobulin-like, plexins, and transcription factors) refers to the tandem domain that constitutes the central stem of TLP-IPT. Glycan-mediated interactions determine the structural assembly of the glycofibrils that lack folded protein component. Our previous and current studies reveal the diversity of the structural folds of glycans, advance our understanding of glycan architecture, and further demonstrate CryoSeek as a structure-first paradigm for discovery.
History
DepositionJan 5, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68132.png

Downloads & links

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Map

FileDownload / File: emd_68132.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of TLP-0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-0.9853612 - 2.4017005
Average (Standard dev.)0.002757919 (±0.07651785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 351.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_68132_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_68132_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TLP-0

EntireName: TLP-0
Components
  • Complex: TLP-0

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Supramolecule #1: TLP-0

SupramoleculeName: TLP-0 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: algae metagenome (others)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 80.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35270
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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