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- EMDB-68070: TLP-2h, a glycofibril obtained from a Karst cave from Guilin City... -

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Basic information

Entry
Database: EMDB / ID: EMD-68070
TitleTLP-2h, a glycofibril obtained from a Karst cave from Guilin City, Guangxi Zhuang Autonomous Region, China
Map data
Sample
  • Complex: dropping water from a Karst cave from Guilin City, Guangxi Province, China
    • Protein or peptide: TLP-2h
Keywordsglycofibril / UNKNOWN FUNCTION
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHu MX / Zhang Q / Chen S / Ge QJ / Wang JW / Yan N / Qin LJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190, 92478205 China
CitationJournal: To Be Published
Title: Absolute hand determination of glycofibrils from natural sources in cryo-EM
Authors: Zhang Q / Qin LJ / Wang TT / Li ZQ / Zhang YL / Chen S / Ge QJ / Yan N / Wang JW / Hu MX
History
DepositionJan 3, 2026-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68070.png

Downloads & links

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Map

FileDownload / File: emd_68070.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 380 pix.
= 355.68 Å		0.94 Å/pix.
x 380 pix.
= 355.68 Å		0.94 Å/pix.
x 380 pix.
= 355.68 Å

Surface

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.18409583 - 0.43796095
Average (Standard dev.)0.0009817246 (±0.011411556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 355.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68070_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_68070_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68070_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : dropping water from a Karst cave from Guilin City, Guangxi Provin...

EntireName: dropping water from a Karst cave from Guilin City, Guangxi Province, China
Components
  • Complex: dropping water from a Karst cave from Guilin City, Guangxi Province, China
    • Protein or peptide: TLP-2h

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Supramolecule #1: dropping water from a Karst cave from Guilin City, Guangxi Provin...

SupramoleculeName: dropping water from a Karst cave from Guilin City, Guangxi Province, China
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)

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Macromolecule #1: TLP-2h

MacromoleculeName: TLP-2h / type: protein_or_peptide / ID: 1
Details: TLP-2h is a macromolecule consisting of a linear chain of A(SEP) dipeptide repeats, surrounded by a polysaccharide coat. We have only built the asymmetric unit of this helical assembly; ...Details: TLP-2h is a macromolecule consisting of a linear chain of A(SEP) dipeptide repeats, surrounded by a polysaccharide coat. We have only built the asymmetric unit of this helical assembly; accordingly, this unit contains a single dipeptide repeat, namely A(SEP).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 256.15 Da
SequenceString:
A(SEP)

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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: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 93.78 Å
Applied symmetry - Helical parameters - Δ&Phi: 6.14 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5082
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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