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Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient, polymorph 2

Analyse Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SAR
Type: protein
Length: 1,350 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transmembrane protein 106B
UniProt: Q9NUM4
Ligands: NAG
Pockets: 18 · best druggability 0.76

Structure

electron microscopy · 1 distinct chain · 0% helix, 81% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Transmembrane protein 106B	protein	135	0% helix, 81% strand	Q9NUM4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, D, F, B, C, E, H, G, J, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.76	0.84	40	empty
2	363	0.76	0.86	43	empty
3	644	0.76	0.82	47	empty
4	420	0.76	0.84	40	empty
5	630	0.74	0.81	47	empty

Interfaces

14 interfaces between chains.

E–J · 5950 Å² buried · 196 hydrogen bonds · protein-protein
B–C · 5948 Å² buried · 195 hydrogen bonds · protein-protein
B–E · 5948 Å² buried · 197 hydrogen bonds · protein-protein
C–H · 5946 Å² buried · 197 hydrogen bonds · protein-protein
A–D · 5937 Å² buried · 196 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

7SAR · Cryo-EM structure of TMEM106B fibrils extracted from a FTLD-TDP patient, polymorph 2 · the same entry in another collection · chain J against J, TM-score 1.00
Q9NUM4 · AlphaFold monomer V2.0 prediction for transmembrane protein 106B (Q9NUM4) · a predicted model of the same protein · chain A against A, TM-score 0.22

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9NUM4
Elsewhere: RCSB PDB 7SAR · PDBe 7SAR · UniProt Q9NUM4

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