4Y0F: Human TDP-43 RRM1 Domain

Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA. Determined by X-ray diffraction at 2.65 Å resolution. Released 10 Feb 2016.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,590
Mol. weight: 30.31 kDa
Released: 10 Feb 2016

Explore 4Y0F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y0F contains 4 α-helices and 12 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.

Chains A and B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	106-109	4	1
α-helix	117-124	8
β-strand	130-137	8	1
β-strand	144-152	9	1
α-helix	155-162	8
β-strand	166-168	3	2
β-strand	171-173	3	2
β-strand	174-176	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TAR DNA-binding protein 43	A, B	protein	103	Homo sapiens	Q13148 (AlphaFold model)
DNA (5'-d(gptptpgpapgpcpgptpt)-3')	C, D	DNA	10	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>4Y0F_1 TAR DNA-binding protein 43 (chains A, B)
MRGSHHHHHHGSQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG
FVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSR

Sequence of entity 2 (C, D), FASTA

>4Y0F_2 DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3') (chains C, D)
GTTGAGCGTT

Primary citation

Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation. Chiang, C.H., Grauffel, C., Wu, L.S. et al. Sci Rep (2016) 6:21581-21581. DOI 10.1038/srep21581 · 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,…
5MDI 2.1 Å, Crystal structure of TDP-43 N-terminal domain at 2.1 A resolution
7N9H 2.2 Å, Structure of the mammalian importin a1 bound to the TDP-43 NLS

Browse structure collections

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