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- EMDB-60656: Cryo-EM structure of TLP-1a -

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Basic information

Entry
Database: EMDB / ID: EMD-60656
TitleCryo-EM structure of TLP-1a
Map dataEM map of TLP-1
Sample
  • Complex: TLP-1a
    • Protein or peptide: TLP-1
KeywordsFibril / PROTEIN FIBRIL
Biological speciesalgae metagenome (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.22 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: 2024
Title: CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy.
Authors: Tongtong Wang / Zhangqiang Li / Kui Xu / Wenze Huang / Gaoxingyu Huang / Qiangfeng Cliff Zhang / Nieng Yan /
Abstract: Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy ...Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM) to analyze filtered water samples collected from the Tsinghua Lotus Pond. Here, we report the structural determination and characterization of two highly similar helical fibrils, named TLP-1a and TLP-1b, each approximately 8 nm in diameter with a 15-Å wide tunnel. These fibrils are assembled from a similar protein protomer, whose structure was conveniently automodeled in CryoNet. The protomer structure does not match any available experimental structures, but shares the same fold as many predicted structures of unknown functions. The amino-terminal β strand of protomer n + 4 inserts into a cleft in protomer n to complete an immunoglobulin (Ig)-like domain. This packing mechanism, known as donor-strand exchange (DSE), has been observed in several bacterial pilus assemblies, wherein the donor is protomer n + 1. Despite distinct shape and thickness, this reminiscence suggests that TLP-1a/b fibrils may represent uncharacterized bacterial pili. Our study demonstrates an emerging paradigm in structural biology, where high-resolution structural determination precedes and drives the identification and characterization of completely unknown objects.
History
DepositionJun 27, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60656.png

Downloads & links

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Map

FileDownload / File: emd_60656.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of TLP-1
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: 0.5
Minimum - Maximum-1.3780801 - 2.4382112
Average (Standard dev.)0.0021768461 (±0.10747397)
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 B map of TLP-1

Fileemd_60656_half_map_1.map
AnnotationHalf_B map of TLP-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map of TLP-1

Fileemd_60656_half_map_2.map
AnnotationHalf_A map of TLP-1
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-1a

EntireName: TLP-1a
Components
  • Complex: TLP-1a
    • Protein or peptide: TLP-1

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Supramolecule #1: TLP-1a

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

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Macromolecule #1: TLP-1

MacromoleculeName: TLP-1 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: algae metagenome (others)
Molecular weightTheoretical: 25.273582 KDa
SequenceString: NLISEQNVTV TMDLQPVLQL GMQGSETVSF VFSQISEYIG GLTQYGAVDL SVSSTVDWCL YAAAFSSDAA DAELNWTNMV TFGDSNPNS ITNLPITVLQ LFQSKPNPDT NSTRDSPSFK TAFDTGRAAL GENNVYASRD PFDRPSADAR YIAGGNAPAE V AGGSYLVD ...String:
NLISEQNVTV TMDLQPVLQL GMQGSETVSF VFSQISEYIG GLTQYGAVDL SVSSTVDWCL YAAAFSSDAA DAELNWTNMV TFGDSNPNS ITNLPITVLQ LFQSKPNPDT NSTRDSPSFK TAFDTGRAAL GENNVYASRD PFDRPSADAR YIAGGNAPAE V AGGSYLVD DGASGSNGAF YFTISFRVVP ALPGTYPRAT SEDQGNTDET DDLVVRGDGR YAYPGVYTLN VKFVMVEC

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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: 11.54 Å
Applied symmetry - Helical parameters - Δ&Phi: 75.13 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16732
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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