9L93: NCOA4

Name: PDB 9L93: Crystal structure of NCOA4 in complex with HERC2
Published: 2025-11-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of NCOA4 in complex with HERC2. Determined by X-ray diffraction at 1.73 Å resolution. Released 5 Nov 2025.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,663
Mol. weight: 48.62 kDa
Ligands: FES
Released: 5 Nov 2025

Explore 9L93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L93 contains 17 α-helices and 24 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: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2554-2556	3
α-helix	2560-2570	11
β-strand	2576-2579	4	1
β-strand	2583	1	2
β-strand	2586	1	2
β-strand	2591-2597	7	1
β-strand	2607-2611	5	1
β-strand	2616-2620	5	1
α-helix	2622-2624	3
β-strand	2625-2629	5	1
α-helix	2630-2633	4
β-strand	2644-2647	4	3
β-strand	2667-2672	6	3
β-strand	2678-2683	6	3
β-strand	2686-2692	7	3
α-helix	2693-2695	3
β-strand	2696-2698	3	3

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2554-2556	3
α-helix	2560-2570	11
β-strand	2576-2579	4	4
β-strand	2583	1	5
β-strand	2586	1	5
β-strand	2591-2597	7	4
β-strand	2607-2611	5	4
β-strand	2616-2620	5	4
α-helix	2622-2624	3
β-strand	2625-2629	5	4
α-helix	2630-2634	5
β-strand	2644-2647	4	6
β-strand	2667-2672	6	6
β-strand	2678-2683	6	6
β-strand	2686-2692	7	6
α-helix	2693-2695	3
β-strand	2696-2698	3	6

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	400-403	4
α-helix	413-415	3
α-helix	422-434	13

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	397-399	3
α-helix	400-403	4
α-helix	413-415	3
α-helix	422-435	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase HERC2	A, B	protein	164	Homo sapiens	O95714
Nuclear receptor coactivator 4	C, D	protein	51	Homo sapiens	Q13772 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9L93_1 E3 ubiquitin-protein ligase HERC2 (chains A, B)
GAMSTGAVVTESQTYKKRADFLSNDDYAVYVRENIQVGMMVRCCRAYEEVCEGDVGKVIK
LDRDGLHDLNVQCDWQQKGGTYWVRYIHVELIGYPPPSSSSHIKIGDKVRVKASVTTPKY
KWGSVTHQSVGVVKAFSANGKDIIVDFPQQSHWTGLLSEMELVP

Sequence of entity 2 (C, D), FASTA

>9L93_2 Nuclear receptor coactivator 4 (chains C, D)
GAMQDPCKVEEVCRANEPCTSFAECVCDENCEKEALYKWLLKKEGKDKNGM

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2

Primary citation

Mechanistic insights into the iron-sulfur cluster-dependent interaction of the autophagy receptor NCOA4 with the E3 ligase HERC2. Liu, H., Shen, L., Gong, X. et al. Proc Natl Acad Sci U S A (2025) 122:e2510269122-e2510269122. DOI 10.1073/pnas.2510269122 · PubMed

Other PDB entries of the same protein (UniProt O95714), best resolution first:

3KCI 1.8 Å, The third RLD domain of HERC2
9L8Y 1.92 Å, Crystal structure of HERC2
7Q42 1.95 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
7RGW 1.99 Å, Crystal structure of HERC2 DOC domain
6WW3 2.1 Å, Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail
7Q45 2.1 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
7Q44 2.2 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
6WW4 2.25 Å, Crystal structure of HERC2 ZZ domain in complex with histone H3 tail
7Q40 2.35 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2
7Q43 2.4 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
7Q46 2.46 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
4L1M 2.6 Å, Structure of the first RCC1-like domain of HERC2

Browse structure collections

About this viewer

MolViewer shows 9L93 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.