PDB-9sa2: The RING domain of IDOL

ID or keywords:

Entry

Database: PDB / ID: 9sa2

Title

The RING domain of IDOL

Components

E3 ubiquitin-protein ligase MYLIP

Keywords

LIGASE / E3 / ubiquitin / RING / Zinc finger

Function / homology

Function and homology information

regulation of low-density lipoprotein particle receptor catabolic process / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / negative regulation of low-density lipoprotein particle clearance / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / positive regulation of protein catabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.1 Å

Authors

Bradshaw, W.J. / He, L. / Guenther, F. / Murphy, E.J.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: The RING domain of IDOL
Authors: Bradshaw, W.J. / He, L. / Guenther, F. / Murphy, E.J.

History

Deposition	Aug 7, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9sa2.cif.gz	164.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9sa2.ent.gz	123.5 KB	Display	PDB format
PDBx/mmJSON format	9sa2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9sa2_validation.pdf.gz	468.9 KB	Display	wwPDB validaton report
Full document	9sa2_full_validation.pdf.gz	472.5 KB	Display
Data in XML	9sa2_validation.xml.gz	22.6 KB	Display
Data in CIF	9sa2_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sa/9sa2 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/9sa2	HTTPS FTP

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Related structure data

Related structure data	9sa1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #88 - Apr 2007 Clathrin similarity (1) #134 - Feb 2011 Integrin similarity (8)

Deposited unit

A: E3 ubiquitin-protein ligase MYLIP

B: E3 ubiquitin-protein ligase MYLIP

C: E3 ubiquitin-protein ligase MYLIP

D: E3 ubiquitin-protein ligase MYLIP

hetero molecules

35.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: E3 ubiquitin-protein ligase MYLIP

B: E3 ubiquitin-protein ligase MYLIP

hetero molecules

defined by author
Evidence: gel filtration
18 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: E3 ubiquitin-protein ligase MYLIP

D: E3 ubiquitin-protein ligase MYLIP

hetero molecules

defined by author
18 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.190, 47.610, 70.540
Angle α, β, γ (deg.)	90.000, 90.858, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	A	A	368 - 437	1 - 70
2	1	1	THR	THR	B	B	368 - 437	1 - 70
3	2	2	LEU	LEU	A	A	368 - 439	1 - 72
4	2	2	LEU	LEU	C	C	368 - 439	1 - 72
5	3	3	HIS	HIS	A	A	368 - 436	1 - 69
6	3	3	HIS	HIS	D	D	368 - 436	1 - 69
7	4	4	THR	THR	B	B	368 - 437	1 - 70
8	4	4	THR	THR	C	C	368 - 437	1 - 70
9	5	5	HIS	HIS	B	B	368 - 436	1 - 69
10	5	5	HIS	HIS	D	D	368 - 436	1 - 69
11	6	6	HIS	HIS	C	C	368 - 436	1 - 69
12	6	6	HIS	HIS	D	D	368 - 436	1 - 69

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	E3 ubiquitin-protein ligase MYLIP / Inducible degrader of the LDL-receptor / Idol / Myosin regulatory light chain interacting protein / ...Inducible degrader of the LDL-receptor / Idol / Myosin regulatory light chain interacting protein / MIR / RING-type E3 ubiquitin transferase MYLIP Mass: 8820.361 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYLIP, BZF1, IDOL, BM-023, PP5242 / Production host: Escherichia coli (E. coli) References: UniProt: Q8WY64, RING-type E3 ubiquitin transferase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Diamond	I03	1	0.9405
SYNCHROTRON	Diamond	I04	2	0.9214

Detector

Type	ID	Detector	Date
DECTRIS EIGER2 XE 16M	1	PIXEL	Jan 19, 2025
DECTRIS EIGER2 XE 16M	2	PIXEL	Feb 1, 2025

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9405	1
2	0.9214	1

Reflection

Resolution: 1.1→70.54 Å / Num. obs: 118793 / % possible obs: 100 % / Redundancy: 49.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.492 / R_pim(I) all: 0.101 / R_rim(I) all: 0.503 / Net I/σ(I): 8.9

Reflection shell

Resolution: 1.1→1.12 Å / Redundancy: 27.5 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5872 / CC_1/2: 0.314 / R_pim(I) all: 3.316 / R_rim(I) all: 12.512 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.1→70.532 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.965 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1741	2012	1.696 %
R_work	0.1423	116610	-
all	0.143	-	-
obs	-	118622	99.865 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 14.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.031 Å²	0 Å²	-0.018 Å²
2-	-	-0.273 Å²	-0 Å²
3-	-	-	0.304 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→70.532 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2246	0	16	419	2681

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2584
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2475
X-RAY DIFFRACTION	r_angle_refined_deg	1.414	1.866	3539
X-RAY DIFFRACTION	r_angle_other_deg	0.803	1.766	5784
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.388	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.927	5	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.566	10	514
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.155	10	116
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	419
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3083
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	577
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	499
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	2146
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	1147
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1266
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.23	0.2	280
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.188	0.2	6
X-RAY DIFFRACTION	r_metal_ion_refined	0.104	0.2	29
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.296	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.312	0.2	124
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.195	0.2	47
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.176	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	4.715	1.343	1259
X-RAY DIFFRACTION	r_mcbond_other	4.69	1.342	1259
X-RAY DIFFRACTION	r_mcangle_it	6.851	2.407	1587
X-RAY DIFFRACTION	r_mcangle_other	6.856	2.41	1588
X-RAY DIFFRACTION	r_scbond_it	7.231	1.737	1325
X-RAY DIFFRACTION	r_scbond_other	7.229	1.737	1326
X-RAY DIFFRACTION	r_scangle_it	10.096	3.029	1915
X-RAY DIFFRACTION	r_scangle_other	10.093	3.029	1916
X-RAY DIFFRACTION	r_lrange_it	17.951	20.895	3009
X-RAY DIFFRACTION	r_lrange_other	15.236	16.934	2852
X-RAY DIFFRACTION	r_rigid_bond_restr	4.042	3	5059
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.112	0.05	2158
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	2164
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.108	0.05	2139
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.133	0.05	2051
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	2138
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.135	0.05	2188

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11219	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.11219	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09623	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09623	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10769	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.10769	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.13331	0.05007
4	8	C	X-RAY DIFFRACTION	Local ncs	0.13331	0.05007
5	9	B	X-RAY DIFFRACTION	Local ncs	0.07905	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.07905	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.13521	0.05007
6	12	D	X-RAY DIFFRACTION	Local ncs	0.13521	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.1-1.129	0.315	154	0.302	8547	0.302	8716	0.926	0.931	99.8279	0.303
1.129-1.159	0.262	112	0.258	8456	0.258	8569	0.947	0.954	99.9883	0.252
1.159-1.193	0.233	142	0.229	8116	0.229	8277	0.963	0.965	99.7704	0.219
1.193-1.23	0.241	149	0.215	7838	0.215	8020	0.963	0.967	99.5885	0.203
1.23-1.27	0.185	141	0.189	7699	0.189	7857	0.981	0.977	99.7836	0.173
1.27-1.315	0.179	158	0.174	7334	0.174	7518	0.976	0.98	99.6542	0.157
1.315-1.364	0.197	152	0.157	7150	0.157	7310	0.976	0.984	99.8906	0.138
1.364-1.42	0.157	152	0.139	6859	0.139	7022	0.984	0.987	99.8433	0.121
1.42-1.483	0.153	119	0.117	6608	0.118	6740	0.986	0.991	99.8071	0.102
1.483-1.555	0.103	86	0.102	6324	0.102	6416	0.994	0.994	99.9065	0.09
1.555-1.639	0.123	110	0.096	6085	0.096	6198	0.992	0.994	99.9516	0.087
1.639-1.739	0.131	85	0.1	5678	0.1	5766	0.989	0.994	99.948	0.092
1.739-1.859	0.131	82	0.102	5392	0.103	5475	0.989	0.994	99.9817	0.096
1.859-2.008	0.154	96	0.11	5001	0.111	5100	0.984	0.993	99.9412	0.105
2.008-2.199	0.133	39	0.113	4636	0.113	4676	0.991	0.992	99.9786	0.11
2.199-2.458	0.137	76	0.11	4177	0.111	4253	0.987	0.993	100	0.11
2.458-2.838	0.188	67	0.125	3703	0.126	3770	0.979	0.991	100	0.129
2.838-3.475	0.201	32	0.137	3151	0.138	3183	0.975	0.988	100	0.145
3.475-4.908	0.144	35	0.135	2469	0.135	2504	0.988	0.99	100	0.152
4.908-70.532	0.312	25	0.229	1386	0.23	1411	0.953	0.967	100	0.249

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