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- PDB-21zt: Cryo-EM structure of TLP-2 -

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Basic information

Entry
Database: PDB / ID: 21zt
TitleCryo-EM structure of TLP-2
ComponentsTLP-2
KeywordsCARBOHYDRATE / Glycofibril
Biological speciesalgae metagenome (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYan, N. / Li, Z. / Wang, T.
Funding support China, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TLP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0095
Polymers6511
Non-polymers21,3584
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/peptide TLP-2


Mass: 650.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) algae metagenome (others)
#2: Polysaccharide
alpha-L-arabinofuranose-(1-4)-alpha-D-mannopyranose-(1-2)-alpha-L-arabinofuranose-(1-2)-beta-L- ...alpha-L-arabinofuranose-(1-4)-alpha-D-mannopyranose-(1-2)-alpha-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-beta-D-xylopyranose-(1-3)-beta-D-glucopyranose-(1-3)][alpha-L-arabinofuranose-(1-6)]alpha-D-mannopyranose-(1-2)-alpha-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-4)-[alpha-L-arabinofuranose-(1-2)]beta-D-xylopyranose-(1-4)][alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-2)]beta-D-xylopyranose-(1-4)-[alpha-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-4)]beta-D-xylopyranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]alpha-D-glucopyranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-2)-[beta-D-glucopyranose-(1-3)]alpha-L-arabinofuranose-(1-4)-[beta-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-2)-[beta-D-xylopyranose-(1-3)]beta-L-arabinofuranose-(1-2)][alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-3)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-3)]2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 5339.562 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/7,38,37/[a2122h-1a_1-5_1*OPO/3O/3=O_2*NCC/3=O][a212h-1b_1-5][a211h-1b_1-4][a211h-1a_1-4][a2122h-1a_1-5][a2122h-1b_1-5][a1122h-1a_1-5]/1-2-2-3-4-3-2-2-4-4-4-4-5-2-4-4-4-6-2-4-4-3-4-7-4-3-4-7-4-6-2-4-4-2-4-2-2-2/a3-b1_a4-s1_b4-c1_c2-d1_c3-h1_c4-j1_d2-e1_d3-g1_e2-f1_h3-i1_j2-k1_j3-r1_k5-l1_l5-m1_m2-n1_m3-q1_n2-o1_n4-p1_s2-t1_s3-v1_s4-H1_t2-u1_v2-w1_w2-x1_x2-y1_x3-D1_x6-G1_y2-z1_z2-A1_A2-B1_B4-C1_D3-E1_E2-F1_H2-I1_H4-J1_J3-K1_K3-L1WURCSPDB2Glycan 1.1.0
[][<O2P1>]{[(1+1)][a-D-GlcpNAc]{[(3+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][b-L-Araf]{[(2+1)][a-L-Araf]{[(2+1)][b-L-Araf]{}}[(3+1)][b-D-Xylp]{}}[(3+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}}[(4+1)][a-L-Araf]{[(2+1)][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-D-Glcp]{[(2+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{}[(4+1)][a-L-Araf]{}}[(3+1)][a-L-Araf]{}}}}[(3+1)][b-D-Glcp]{}}}}[(4+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{[(2+1)][a-L-Araf]{}}[(3+1)][b-L-Araf]{[(2+1)][a-L-Araf]{[(2+1)][a-D-Manp]{[(2+1)][a-L-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-L-Araf]{[(2+1)][a-D-Manp]{[(4+1)][a-L-Araf]{}}}}}[(3+1)][b-D-Glcp]{[(3+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{}}}[(6+1)][a-L-Araf]{}}}}[(4+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{[(3+1)][b-D-Xylp]{[(3+1)][b-D-Xylp]{}}}}}}}LINUCSPDB-CARE
Has ligand of interestN
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-2 / Type: COMPLEX / Entity ID: #1 / 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: TFS 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

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 108.7 ° / Axial rise/subunit: 6.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16082 / Symmetry type: HELICAL

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