9IIC: HOIP RING2-LDD

Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain. Determined by X-ray diffraction at 2.78 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,009
Mol. weight: 117.96 kDa
Ligands: ZN
Released: 25 Jun 2025

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

Secondary structure: helices and β-sheets

9IIC contains 56 α-helices and 34 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: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
β-strand	30-37	8	6
β-strand	43-49	7	6
β-strand	55-61	7	6
α-helix	67-79	13
β-strand	85	1	7
β-strand	88-93	6	6
β-strand	98-103	6	6
β-strand	109	1	7
α-helix	110-117	8
α-helix	120-122	3
α-helix	123-142	20
α-helix	152-154	3
β-strand	155-157	3	7
β-strand	163-165	3	7
α-helix	193-196	4
α-helix	205-219	15
α-helix	229-238	10
α-helix	240-242	3
α-helix	247-249	3
α-helix	252-261	10
α-helix	270-271	2
α-helix	272-275	4
α-helix	279-282	4
α-helix	284-286	3
α-helix	287-290	4
α-helix	291-307	17

Chain B: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	27-29	3
β-strand	30-38	9	1
β-strand	43-49	7	1
β-strand	55-61	7	1
α-helix	67-78	12
β-strand	85	1	2
β-strand	88-94	7	1
β-strand	97-103	7	1
β-strand	108-109	2	2
α-helix	110-117	8
α-helix	120-122	3
α-helix	123-142	20
α-helix	152-154	3
β-strand	155-157	3	2
β-strand	163-165	3	2
α-helix	193-196	4
α-helix	205-219	15
α-helix	229-238	10
α-helix	240-242	3
α-helix	247-249	3
α-helix	252-261	10
α-helix	270-271	2
α-helix	272-276	5
α-helix	279-282	4
α-helix	284-286	3
α-helix	287-290	4
α-helix	291-308	18

Chain C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	860-867	8
β-strand	869-871	3	3
β-strand	876-878	3	3
β-strand	887-889	3	4
β-strand	896-898	3	4
β-strand	904	1	4
α-helix	931-934	4
α-helix	939-948	10
α-helix	957-958	2
β-strand	972-977	6	5
β-strand	980-985	6	5
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1039-1041	3
α-helix	1046-1060	15
α-helix	1062-1064	3

Chain D: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	860-867	8
β-strand	869-870	2	8
β-strand	877-878	2	8
β-strand	887-889	3	9
β-strand	896-898	3	9
β-strand	904	1	9
β-strand	907	1	10
β-strand	922	1	10
α-helix	931-934	4
α-helix	939-948	10
α-helix	957-958	2
β-strand	972-977	6	11
β-strand	980-985	6	11
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1046-1060	15
α-helix	1062-1064	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase 4 37kDa subunit	A, B	protein	302	Homo sapiens	Q13043 (AlphaFold model)
E3 ubiquitin-protein ligase RNF31	C, D	protein	215	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9IIC_1 Serine/threonine-protein kinase 4 37kDa subunit (chains A, B)
FRRQLKKLDEDSLTKQPEEVFDVLEKLGEGSYGSVYKAIHKETGQIVAIRQVPVESDLQE
IIKEISIMQQCDSPHVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLTEDEIATI
LQSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPF
WMAPEVIQEIGYNCVADIWSLGITAIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPEL
WSDNFTDFVKQCLVKSPEQRATATQLLQHPFVRSAKGVSILRDLINEAMDVKLKRQESQQ
RE

Sequence of entity 2 (C, D), FASTA

>9IIC_2 E3 ubiquitin-protein ligase RNF31 (chains C, D)
AQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNC
RVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKE
VPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHV
RPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

STK4 inhibits the E3 activity of HOIP by phosphorylating its allosteric ubiquitin-binding site. Wang, Y., Zhou, X., Lin, Z. et al. Cell Discov (2025) 11:75-75. DOI 10.1038/s41421-025-00824-x · PubMed

Other PDB entries of the same protein (UniProt Q13043 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAV 1.9 Å, Crystal structure of MST1 with a MAP4K1 SMOL inhibitor
4NR2 2.0 Å, Crystal structure of STK4 (MST1) SARAH domain
8A5J 2.12 Å, Crystal structure of Human STE20-like kinase 1, MST1 in complex with compound XMU-MP-1
8PAW 2.14 Å, Crystal structure of MST1 with a MAP4K1 SMOL inhibitor
3COM 2.2 Å, Crystal structure of Mst1 kinase
4OH8 2.28 Å, Crystal Structure of the human MST1-RASSF5 SARAH heterodimer
5TWG 2.3 Å, human MOB1A bound to human MST1 phosphorylated T353 peptide
9VX3 2.39 Å, Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp
5TWH 2.5 Å, human MOB1A bound to MST1 phosphorylated T367 peptide
7CEA 2.55 Å, Crystal structure of HUTS-4 Fv-clasp fragment
6YAT 2.58 Å, Crystal structure of STK4 (MST1) in complex with compound 6
7CEB 2.89 Å, Crystal structure of alpha6beta1 integrin headpiece

Browse structure collections

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