PDB-9bcc: Structure of KLHDC2 bound to SJ46418

ID or keywords:

Entry

Database: PDB / ID: 9bcc

Title

Structure of KLHDC2 bound to SJ46418

Components

Kelch domain-containing protein 2

Keywords

LIGASE/INHIBITOR / Kelch domain / inhibitor / complex / KLHDC2 / LIGASE / LIGASE-INHIBITOR complex

Function / homology

Function and homology information

ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear body / nucleoplasm / nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Scott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Lee, H.W. ...

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01CA247365-04	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01-AI157312	United States

Citation

Journal: Nat Commun / Year: 2024
Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2.
Authors: Scott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Yang, L. / Li, Y. / Loudon, V.C. / Lee, H.W. / Ochoada, J. / ...

History

Deposition	Apr 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bcc.cif.gz	283.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9bcc.ent.gz		Display	PDB format
PDBx/mmJSON format	9bcc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bc/9bcc ftp://data.pdbj.org/pub/pdb/validation_reports/bc/9bcc	HTTPS FTP

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Related structure data

Related structure data	9bc9C 9bcaC 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	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Kelch domain-containing protein 2

B: Kelch domain-containing protein 2

hetero molecules

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

1

A: Kelch domain-containing protein 2

hetero molecules

defined by author
40.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Kelch domain-containing protein 2

hetero molecules

defined by author
40.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.565, 88.292, 89.265
Angle α, β, γ (deg.)	90.00, 104.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1 Mass: 39764.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2U9
#2: Chemical	ChemComp-A1APT / N-({2-[8-(2-methoxyethoxy)naphthalen-2-yl]-1,3-thiazol-4-yl}acetyl)glycine / SJ46418 Mass: 400.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₀N₂O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NCO / COBALT HEXAMMINE(III) Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH₁₈N₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.14 Å³/Da / Density % sol: 42.51 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 13-18% PEG3350, 0.2M NaSCN, 0.1 M Bis-Tris Propane, pH = 7.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-1 / Wavelength: 0.9201 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9201 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 73315 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC_1/2: 0.988 / CC star: 0.997 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.052 / R_rim(I) all: 0.102 / Χ²: 1.336 / Net I/σ(I): 8.6 / Num. measured all: 267252

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.76	3.4	0.377	7260	0.815	0.948	0.234	0.445	0.366	99
1.76-1.83	3.3	0.305	7269	0.87	0.965	0.195	0.363	0.465	99.9
1.83-1.91	3.6	0.246	7336	0.912	0.977	0.148	0.288	0.59	99.8
1.91-2.02	3.6	0.196	7354	0.936	0.983	0.118	0.23	0.911	99.9
2.02-2.14	3.6	0.158	7292	0.954	0.988	0.096	0.186	1.197	99.8
2.14-2.31	3.9	0.136	7328	0.969	0.992	0.079	0.158	1.476	99.8
2.31-2.54	3.9	0.116	7321	0.974	0.993	0.067	0.134	1.77	99.7
2.54-2.91	3.8	0.094	7297	0.981	0.995	0.055	0.109	2.054	99.5
2.91-3.66	3.5	0.069	7390	0.988	0.997	0.042	0.081	2.349	99.7
3.66-50	3.9	0.054	7468	0.993	0.998	0.031	0.063	1.87	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→39.32 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2397	3579	4.89 %
R_work	0.2044	-	-
obs	0.206	73166	99.24 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→39.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5238	0	63	531	5832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5486
X-RAY DIFFRACTION	f_angle_d	0.823	7467
X-RAY DIFFRACTION	f_dihedral_angle_d	16.273	1910
X-RAY DIFFRACTION	f_chiral_restr	0.055	745
X-RAY DIFFRACTION	f_plane_restr	0.008	958

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.72	0.3309	145	0.2921	2400	X-RAY DIFFRACTION	90
1.72-1.74	0.2863	141	0.2643	2618	X-RAY DIFFRACTION	99
1.74-1.77	0.3101	121	0.2466	2694	X-RAY DIFFRACTION	99
1.77-1.8	0.2657	136	0.2378	2672	X-RAY DIFFRACTION	99
1.8-1.82	0.2466	130	0.2257	2675	X-RAY DIFFRACTION	99
1.82-1.85	0.2607	160	0.2154	2658	X-RAY DIFFRACTION	100
1.85-1.89	0.267	140	0.2136	2625	X-RAY DIFFRACTION	99
1.89-1.92	0.2537	153	0.2015	2676	X-RAY DIFFRACTION	100
1.92-1.96	0.2052	125	0.2047	2716	X-RAY DIFFRACTION	100
1.96-2	0.2632	117	0.1962	2673	X-RAY DIFFRACTION	100
2-2.04	0.2272	148	0.2031	2690	X-RAY DIFFRACTION	100
2.04-2.09	0.2171	158	0.2071	2662	X-RAY DIFFRACTION	100
2.09-2.14	0.2577	145	0.2024	2690	X-RAY DIFFRACTION	100
2.14-2.2	0.2487	173	0.1946	2658	X-RAY DIFFRACTION	100
2.2-2.26	0.2163	147	0.1957	2659	X-RAY DIFFRACTION	100
2.26-2.34	0.2574	170	0.1981	2669	X-RAY DIFFRACTION	100
2.34-2.42	0.2458	133	0.2065	2692	X-RAY DIFFRACTION	100
2.42-2.52	0.3064	130	0.2144	2691	X-RAY DIFFRACTION	100
2.52-2.63	0.2369	116	0.2187	2724	X-RAY DIFFRACTION	99
2.63-2.77	0.26	131	0.2112	2700	X-RAY DIFFRACTION	100
2.77-2.94	0.2536	123	0.214	2693	X-RAY DIFFRACTION	100
2.94-3.17	0.2406	123	0.2043	2706	X-RAY DIFFRACTION	100
3.17-3.49	0.2456	147	0.2025	2693	X-RAY DIFFRACTION	100
3.49-3.99	0.2298	126	0.1888	2727	X-RAY DIFFRACTION	100
3.99-5.03	0.1911	105	0.1786	2760	X-RAY DIFFRACTION	100
5.03-39.32	0.2033	136	0.2046	2766	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4221	-0.0626	-0.337	0.2496	-0.0718	0.5364	-0.0054	0.1785	0.0215	-0.0072	-0.0258	-0.0419	-0.0461	0.1377	-0.0339	0.0872	-0.0465	-0.0184	0.0914	0.0314	0.092	12.2925	4.7416	12.9595
2	0.1616	-0.0923	-0.181	0.0865	0.1687	0.2279	-0.0689	-0.0101	-0.2162	-0.022	-0.0241	0.0235	0.0788	0.1385	-0.0341	0.0956	-0.0094	-0.0013	0.0445	-0.0526	0.165	8.3502	-14.354	19.0831
3	0.8689	-0.1545	-0.3798	0.4887	0.0963	0.7319	-0.0667	-0.1968	0.04	0.0958	0.057	0.0161	-0.0077	0.0522	-0.011	0.0924	-0.0049	-0.0082	0.0962	-0.0224	0.0856	7.0288	-1.4086	30.6766
4	0.1254	-0.0615	0.2777	0.1338	0.0361	0.622	-0.0226	-0.1716	-0.0561	0.0244	-0.0039	0.0446	0.0873	0.1338	-0.0278	0.1033	0.0496	0.0176	0.1037	0.0321	0.0916	12.1349	-7.8106	-11.9959
5	0.2283	0.1023	0.1048	0.2098	-0.2544	0.3938	-0.1751	0.1281	-0.0282	0.0464	0.1093	0.1562	-0.1231	0.0955	-0.0114	0.0665	0.0533	0.0019	0.0115	-0.0201	0.1434	8.1738	11.3974	-17.6637
6	0.9915	0.1661	0.3319	0.3392	0.0761	0.8626	-0.0786	0.166	-0.0344	-0.0577	0.0762	0.0184	-0.0082	0.039	-0	0.0913	-0.004	0.0077	0.0735	-0.0033	0.0823	7.6467	-0.0133	-30.2903
7	0.1218	0.0208	0.1766	0.004	0.0343	0.1457	-0.1254	0.0592	-0.2803	-0.012	0.0056	0.2622	0.2319	-0.2983	0.0003	0.1952	-0.0125	0.0011	0.1399	0.0121	0.188	-1.581	-13.0193	-23.1446

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 148 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 149 through 189 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 190 through 360 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 26 through 148 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 149 through 189 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 190 through 344 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 345 through 360 )

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