5MDI: TDP-43 N-terminal domain

Crystal structure of TDP-43 N-terminal domain at 2.1 A resolution. Determined by X-ray diffraction at 2.1 Å resolution. Released 5 Jul 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,344
Mol. weight: 22.95 kDa
Released: 5 Jul 2017

Explore 5MDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MDI contains 7 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
β-strand	16-19	4	1
β-strand	26-27	2	2
α-helix	28-32	5
β-strand	40-44	5	1
β-strand	51-53	3	1
α-helix	54	1
β-strand	55-57	3	2
β-strand	60-62	3	2
α-helix	71	1
β-strand	72-76	5	1

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	14-15	2
β-strand	16-19	4	1
β-strand	26-27	2	3
α-helix	28-32	5
β-strand	40-44	5	1
β-strand	51-53	3	1
α-helix	54	1
β-strand	55-57	3	3
β-strand	60-62	3	3
α-helix	71	1
β-strand	72-76	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TAR DNA-binding protein 43	A, B	protein	102	Homo sapiens	Q13148 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5MDI_1 TAR DNA-binding protein 43 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMASSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGA
CGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKD

Primary citation

Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Afroz, T., Hock, E.M., Ernst, P. et al. Nat Commun (2017) 8:45-45. DOI 10.1038/s41467-017-00062-0 · PubMed

Other PDB entries of the same protein (UniProt Q13148 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CF4 0.75 Å, Segment NFGTFS, with familial mutation A315T and phosphorylated threonine, from the low…
5WHP 1.0 Å, Crystal structure of the segment, NFGTFS, from the A315T familial variant of the low…
5WKB 1.0 Å, MicroED structure of the segment, NFGEFS, from the A315E familial variant of the low…
5WIA 1.0 Å, Crystal structure of the segment, GNNSYS, from the low complexity domain of TDP-43,…
5WHN 1.1 Å, Crystal structure of the segment, NFGAFS, from the low complexity domain of TDP-43,…
5WIQ 1.25 Å, Crystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43,…
5W50 1.4 Å, Crystal structure of the segment, LIIKGI, from the RRM2 of TDP-43, residues 248-253
5W52 1.4 Å, MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257
6CFH 1.5 Å, SWGMMGMLASQ segment from the low complexity domain of TDP-43
5WKD 1.8 Å, Crystal structure of the segment, GNNQGSN, from the low complexity domain of TDP-43,…
7N9H 2.2 Å, Structure of the mammalian importin a1 bound to the TDP-43 NLS
8CG3 2.39 Å, Structure of TDP-43 amyloid filament from type A FTLD-TDP (variant 1)

Browse structure collections

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