21XM | pdb_000021xm

TLP-2h, a glycofibril obtained from a Karst cave from Guilin City, Guangxi Zhuang Autonomous Region, China

PDB DOI: https://doi.org/10.2210/pdb21XM/pdb
EM Map EMD-68070: EMDB EMDataResource

Classification: UNKNOWN FUNCTION
Organism(s): unidentified
Mutation(s): No

Deposited: 2026-01-03 Released: 2026-02-18
Deposition Author(s): Hu, M.X., Zhang, Q., Chen, S., Ge, Q.J., Wang, J.W., Yan, N., Qin, L.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 21XM

This is version 1.0 of the entry. See complete history.

Literature

Absolute hand determination of glycofibrils from natural sources in cryo-EM

Zhang, Q., Qin, L.J., Wang, T.T., Li, Z.Q., Zhang, Y.L., Chen, S., Ge, Q.J., Yan, N., Wang, J.W., Hu, M.X.

To be published.

Macromolecule Content

Total Structure Weight: 4.55 kDa
Atom Count: 304
Modeled Residue Count: 2
Deposited Residue Count: 2
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TLP-2h	A	2	unidentified	Mutation(s): 0

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-2)-[beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-2)]beta-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	19		N/A	Interactions Focus chain B Interactions & Density Focus chain B

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose	C	7		N/A	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371254, 32171190, 92478205

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.