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- PDB-9ikk: Cryo-EM structure of TLP-1b -

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Basic information

Entry
Database: PDB / ID: 9ikk
TitleCryo-EM structure of TLP-1b
ComponentsTLP-2
KeywordsPROTEIN FIBRIL / Fibril
Biological speciesalgae metagenome (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsYan, N. / Yan, C. / Li, Z. / Wang, T.
Funding support China, 3items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TLP-2
B: TLP-2
C: TLP-2
D: TLP-2
E: TLP-2
F: TLP-2
G: TLP-2
H: TLP-2
I: TLP-2
J: TLP-2
K: TLP-2
L: TLP-2
M: TLP-2
N: TLP-2
O: TLP-2
P: TLP-2


Theoretical massNumber of molelcules
Total (without water)404,63216
Polymers404,63216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
TLP-2


Mass: 25289.490 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) algae metagenome (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: TLP-1b / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: algae metagenome (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 78.06 ° / Axial rise/subunit: 12.33 Å / Axial symmetry: C1
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9182 / Symmetry type: HELICAL

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