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- PDB-21xk: TLP-2f, a glycofibril obtained from a Karst cave from Guilin City... -

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Basic information

Entry
Database: PDB / ID: 21xk
TitleTLP-2f, a glycofibril obtained from a Karst cave from Guilin City, Guangxi Zhuang Autonomous Region, China
ComponentsTLP-2f
KeywordsUNKNOWN FUNCTION / glycofibril
Biological speciesunidentified (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsHu, M.X. / Zhang, Q. / Chen, S. / Ge, Q.J. / Wang, J.W. / Yan, N. / Qin, L.J.
Funding support China, 1items
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: Hu, M.X. / Zhang, Q. / Chen, S. / Ge, Q.J. / Wang, J.W. / Yan, N. / Qin, L.J.
History
DepositionJan 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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-2f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4764
Polymers1761
Non-polymers6,3003
Water00
1
A: TLP-2f
hetero molecules
x 30


Theoretical massNumber of molelcules
Total (without water)194,272120
Polymers5,28530
Non-polymers188,98790
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation29

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Components

#1: Protein/peptide TLP-2f


Mass: 176.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: TLP-2f is a macromolecule consisting of a linear chain of SA dipeptide repeats, surrounded by a polysaccharide coat. We have only built the asymmetric unit of this helical assembly; ...Details: TLP-2f is a macromolecule consisting of a linear chain of SA 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 SA.
Source: (natural) unidentified (others)
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-2)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 2856.513 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3DManpb1-6[DManpb1-4]DManpb1-2DManpb1-6DManpb1-4[DManpb1-6]DManpb1-3[DManpa1-2DManpb1-3DManpb1-6DManpb1-6]DGlcpNAca1-3[DGlcpNAcb1-2DManpa1-2]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,17,16/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-3-4-4-4-4-4-4-1-1-4-4-4-4-1/a2-b1_a3-d1_b2-c1_d3-e1_d6-n1_e4-f1_e6-m1_f6-g1_g2-h1_h4-i1_h6-j1_j3-k1_k6-l1_n6-o1_o3-p1_p2-q1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(3+1)][a-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}[(6+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[beta-D-mannopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[beta-D-mannopyranose-(1-2)]beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 1397.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-3[DManpb1-2]DManpb1-4[DManpb1-3]DGlcpNAca1-3[DManpb1-4]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-3-3-4-3-3/a3-b1_a4-h1_b3-c1_b4-d1_d2-e1_d3-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-GlcpNAc]{[(3+1)][b-D-Manp]{}[(4+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)][beta-D-mannopyranose-(1-2)][beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-2)-[beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2045.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-2DManpb1-4[DManpb1-2DManpb1-3][DManpb1-2][DManpb1-6]DManpb1-2[DManpb1-6DManpb1-4]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,12,11/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2-2-2-3-1-2-2-2/a4-b1_b2-c1_b4-k1_c2-d1_c3-e1_c4-g1_c6-j1_e2-f1_g2-h1_h2-i1_k6-l1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}[(6+1)][b-D-Manp]{}}[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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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: dropping water from a Karst cave from Guilin City, Guangxi Province, China
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified (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: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 132.05 ° / Axial rise/subunit: 5.54 Å / Axial symmetry: C1
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16645 / Symmetry type: HELICAL

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