8YFK: FIP200 claw/TNIP1_FIR_pS123

Crystal structure of FIP200 claw/TNIP1_FIR_pS123. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 3,516
Mol. weight: 53.4 kDa
Ligands: MG
Released: 14 Aug 2024

Explore 8YFK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YFK contains 11 α-helices and 34 β-strands across 8 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, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1495-1496	2	1
β-strand	1506-1512	7	1
β-strand	1517-1520	4	1
β-strand	1528-1530	3	1
α-helix	1531	1
α-helix	1532-1534	3
α-helix	1536-1538	3
β-strand	1554-1567	14	1
β-strand	1581-1588	8	1

Chains B, D, F and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	106-108	3	1

Chain C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1495-1497	3	4
β-strand	1506-1512	7	4
β-strand	1517-1520	4	4
β-strand	1528-1530	3	4
α-helix	1531	1
α-helix	1532-1534	3
β-strand	1554-1567	14	4
β-strand	1581-1588	8	4

Chains E and G: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	1496-1497	2	4
β-strand	1506-1512	7	4
β-strand	1517-1520	4	4
β-strand	1528-1530	3	4
α-helix	1531	1
α-helix	1535-1537	3
β-strand	1541	1	5
β-strand	1545	1	4
α-helix	1548-1551	4
β-strand	1554	1	5
β-strand	1555-1567	13	4
β-strand	1581-1589	9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RB1-inducible coiled-coil protein 1	A, C, E, G	protein	105	Homo sapiens	Q8TDY2 (AlphaFold model)
TNIP1_FIR_pS123 peptide	B, D, F, H	protein	11	Homo sapiens	Q15025 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8YFK_1 RB1-inducible coiled-coil protein 1 (chains A, C, E, G)
SRHSEKIAIRDFQVGDLVLIILDERHDNYVLFTVSPTLYFLHSESLPALDLKPGEGASGA
SRRPWVLGKVMEKEYCQAKKAQNRFKVPLGTKFYRVKAVSWNKKV

Sequence of entity 2 (B, D, F, H), FASTA

>8YFK_2 TNIP1_FIR_pS123 peptide (chains B, D, F, H)
SSGTSSEFEVV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (MPD) are not listed.

Primary citation

Structural basis for TNIP1 binding to FIP200 during mitophagy. Wu, S., Li, M., Wang, L. et al. J Biol Chem (2024) 300:107605-107605. DOI 10.1016/j.jbc.2024.107605 · PubMed

Other PDB entries of the same protein (UniProt Q8TDY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7D0E 1.4 Å, Crystal structure of FIP200 Claw/p-CCPG1 FIR2
9D34 1.42 Å, FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1…
8YFL 1.5 Å, crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123
8YFM 1.5 Å, Crystal structure of FIP200 claw/TNIP1_FIR_pS122
6DCE 1.56 Å, X-ray structure of FIP200 claw domain
9J54 1.61 Å, Crystal structure of FIP200 Claw in complex with ATG16L1
7CZG 1.8 Å, Crystal structure of FIP200 Claw domain apo form
9LUA 1.97 Å, Crystal structure of FIP200 Claw domain and SMCR8 FIR motif complex
7CZM 2.0 Å, Crystal structure of FIP200 Claw/p-OPtineurin LIR complex
7EA2 2.14 Å, crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain
8YFN 2.3 Å, Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an…
8W6B 2.39 Å, crystal structure of TAX1BP1 SKICH domain in complex with RB1CC1 coiled-coil domain

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