9HFU: Caprin1 peptide

Caprin1 peptide bound to SPOP MATH domain. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Apr 2025.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,720
Mol. weight: 36.23 kDa
Released: 23 Apr 2025

Explore 9HFU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HFU contains 12 α-helices and 22 β-strands across 4 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: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	1
α-helix	41-43	3
β-strand	52-53	2	2
α-helix	54-56	3
β-strand	57	1	2
β-strand	66-72	7	2
α-helix	78-80	3
β-strand	83-92	10	2
β-strand	98-107	10	1
β-strand	113-118	6	1
β-strand	123-125	3	1
β-strand	130-138	9	2
α-helix	139-143	5
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-165	11	1

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	3
α-helix	41-43	3
β-strand	52-53	2	4
α-helix	54-56	3
β-strand	57	1	4
β-strand	66-72	7	4
α-helix	78-80	3
β-strand	83-92	10	4
β-strand	98-107	10	3
β-strand	113-118	6	3
β-strand	123-125	3	3
β-strand	130-138	9	4
α-helix	139-142	4
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-164	10	3

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	436	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Speckle type BTB/POZ protein	A, B	protein	141	Homo sapiens	D6RDG8 (AlphaFold model)
Caprin-1	C, D	protein	17	Homo sapiens	Q14444 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9HFU_1 Speckle type BTB/POZ protein (chains A, B)
APKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLS
LYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDE
ANGLLPDDKLTLFCEVSVVQD

Sequence of entity 2 (C, D), FASTA

>9HFU_2 Caprin-1 (chains C, D)
QPEATQVPLVSSTSEGY

Primary citation

Sequence rules for a long SPOP-binding degron required for protein ubiquitylation. Makhlouf, L., Mishra, M., Makhlouf, H. et al. Biochem J (2025) 482:583-600. DOI 10.1042/BCJ20253041 · PubMed

Other PDB entries of the same protein (UniProt D6RDG8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KPI 1.7 Å, Crystal structure of the SPOP MATH domain
9HFW 1.7 Å, SRC-3 (NCoA-3) peptide bound to SPOP MATH domain
7KPK 1.71 Å, Crystal structure of the SPOP MATH domain in complex with a fragment of Pdx1
9HGH 1.9 Å, MyD88 peptide_1 bound to SPOP MATH domain

Browse structure collections

About this viewer

MolViewer shows 9HFU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.