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- EMDB-60659: Cryo-EM structure of TLP-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-60659
TitleCryo-EM structure of TLP-4
Map dataCryo-EM map of TLP-4
Sample
  • Complex: TLP-4
    • Protein or peptide: TLP-4
KeywordsFibril / PROTEIN FIBRIL
Biological speciesalgae metagenome (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYan N / Yan C / Li Z / Wang T
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32330052 China
National Natural Science Foundation of China (NSFC)32341016 China
National Natural Science Foundation of China (NSFC)32171204 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: CryoSeek II: Cryo-EM analysis of glycofibrils from freshwater reveals well-structured glycans coating linear tetrapeptide repeats.
Authors: Tongtong Wang / Wenze Huang / Kui Xu / Yitong Sun / Qiangfeng Cliff Zhang / Chuangye Yan / Zhangqiang Li / Nieng Yan /
Abstract: Despite the recent breakthrough in structure determination and prediction of proteins, the structural investigation of carbohydrates remains a challenge. Here, we report the cryo-EM analysis of a ...Despite the recent breakthrough in structure determination and prediction of proteins, the structural investigation of carbohydrates remains a challenge. Here, we report the cryo-EM analysis of a glycofibril found in the freshwater in the Tsinghua Lotus Pond. The fibril, which we name TLP-4, is made of a linear chain of tetrapeptide repeats coated with >4 nm thick glycans. In each repeat, two glycans are O-linked to a 3,4-dihydroxyproline and another glycan attaches to the adjacent Ser or Thr. The fibril structure is entirely maintained through glycan packing. Bioinformatic analysis confirms the conservation of the TLP-4 repeats across species, suggesting the existence of a large number of glycofibrils to be discovered. Our findings not only provide valuable insights into the structural roles of glycans in bio-assemblies but also demonstrate the potential of our recently formulated research strategy of CryoSeek to find bioentities and establish prototypes for structural studies of carbohydrates.
History
DepositionJun 27, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60659.png

Downloads & links

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Map

FileDownload / File: emd_60659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of TLP-4
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: 0.2
Minimum - Maximum-0.79287744 - 2.402559
Average (Standard dev.)0.0009564067 (±0.05093104)
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 A map of TLP-4

Fileemd_60659_half_map_1.map
AnnotationHalf_A map of TLP-4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of TLP-4

Fileemd_60659_half_map_2.map
AnnotationHalf_B map of TLP-4
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-4

EntireName: TLP-4
Components
  • Complex: TLP-4
    • Protein or peptide: TLP-4

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Supramolecule #1: TLP-4

SupramoleculeName: TLP-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: algae metagenome (others)

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Macromolecule #1: TLP-4

MacromoleculeName: TLP-4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: algae metagenome (others)
Molecular weightTheoretical: 7.008729 KDa
SequenceString:
(A1D9O)TAS(A1D9O)TAS(A1D9O)T AS(A1D9O)TAS(A1D9O)TAS (A1D9O)TAS(A1D9O)TAS(A1D9O)T AS (A1D9O)TAS(A1D9O)TA S(A1D9O)TAS(A1D9O)TAS(A1D9O) TAS(A1D9O)TAS(A1D9O)TA S(A1D9O)TAS (A1D9O)TAS (A1D9O)TAS

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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

MicroscopeFEI TITAN 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: 12.41 Å
Applied symmetry - Helical parameters - Δ&Phi: 134.79 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27189
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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