PDB-9gkg: Crystal structure of UNC119 in complex with Squarunkin A

ID or keywords:

Entry

Database: PDB / ID: 9gkg

Title

Crystal structure of UNC119 in complex with Squarunkin A

Components

Protein unc-119 homolog A

Keywords

TRANSPORT PROTEIN / Inhibitor / Complex

Function / homology

Function and homology information

negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / phototransduction / intercellular bridge / visual perception / endocytosis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.21 Å

Authors

Yelland, T. / Ismail, S.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Crystal structure of UNC119 in complex with Squarunkin A
Authors: Yelland, T. / Ismail, S.

History

Deposition	Aug 24, 2024	Deposition site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gkg.cif.gz	228.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9gkg.ent.gz	177.6 KB	Display	PDB format
PDBx/mmJSON format	9gkg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gkg_validation.pdf.gz	916.6 KB	Display	wwPDB validaton report
Full document	9gkg_full_validation.pdf.gz	925.2 KB	Display
Data in XML	9gkg_validation.xml.gz	45.3 KB	Display
Data in CIF	9gkg_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/9gkg ftp://data.pdbj.org/pub/pdb/validation_reports/gk/9gkg	HTTPS FTP

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Related structure data

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

Deposited unit

D: Protein unc-119 homolog A

A: Protein unc-119 homolog A

B: Protein unc-119 homolog A

C: Protein unc-119 homolog A

E: Protein unc-119 homolog A

K: Protein unc-119 homolog A

hetero molecules

130 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Protein unc-119 homolog A

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

2

A: Protein unc-119 homolog A

hetero molecules

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

3

B: Protein unc-119 homolog A

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

4

C: Protein unc-119 homolog A

hetero molecules

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

5

E: Protein unc-119 homolog A

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

6

K: Protein unc-119 homolog A

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.730, 80.630, 191.030
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	GLY	GLY	D	A	59 - 238	1 - 180
2	1	1	PRO	PRO	GLY	GLY	A	B	59 - 238	1 - 180
3	2	2	PRO	PRO	GLY	GLY	D	A	59 - 238	1 - 180
4	2	2	PRO	PRO	GLY	GLY	B	C	59 - 238	1 - 180
5	3	3	PRO	PRO	GLY	GLY	D	A	59 - 238	1 - 180
6	3	3	PRO	PRO	GLY	GLY	C	D	59 - 238	1 - 180
7	4	4	PRO	PRO	SER	SER	D	A	59 - 237	1 - 179
8	4	4	PRO	PRO	SER	SER	E	E	59 - 237	1 - 179
9	5	5	ILE	ILE	GLY	GLY	D	A	60 - 238	2 - 180
10	5	5	ILE	ILE	GLY	GLY	K	F	60 - 238	2 - 180
11	6	6	PRO	PRO	GLY	GLY	A	B	59 - 238	1 - 180
12	6	6	PRO	PRO	GLY	GLY	B	C	59 - 238	1 - 180
13	7	7	PRO	PRO	GLY	GLY	A	B	59 - 238	1 - 180
14	7	7	PRO	PRO	GLY	GLY	C	D	59 - 238	1 - 180
15	8	8	PRO	PRO	SER	SER	A	B	59 - 237	1 - 179
16	8	8	PRO	PRO	SER	SER	E	E	59 - 237	1 - 179
17	9	9	ILE	ILE	GLY	GLY	A	B	60 - 238	2 - 180
18	9	9	ILE	ILE	GLY	GLY	K	F	60 - 238	2 - 180
19	10	10	PRO	PRO	GLY	GLY	B	C	59 - 238	1 - 180
20	10	10	PRO	PRO	GLY	GLY	C	D	59 - 238	1 - 180
21	11	11	PRO	PRO	SER	SER	B	C	59 - 237	1 - 179
22	11	11	PRO	PRO	SER	SER	E	E	59 - 237	1 - 179
23	12	12	ILE	ILE	GLY	GLY	B	C	60 - 238	2 - 180
24	12	12	ILE	ILE	GLY	GLY	K	F	60 - 238	2 - 180
25	13	13	PRO	PRO	SER	SER	C	D	59 - 237	1 - 179
26	13	13	PRO	PRO	SER	SER	E	E	59 - 237	1 - 179
27	14	14	ILE	ILE	SER	SER	C	D	60 - 237	2 - 179
28	14	14	ILE	ILE	SER	SER	K	F	60 - 237	2 - 179
29	15	15	ILE	ILE	TYR	TYR	E	E	60 - 236	2 - 178
30	15	15	ILE	ILE	TYR	TYR	K	F	60 - 236	2 - 178

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
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Protein unc-119 homolog A / Retinal protein 4 / hRG4 Mass: 21402.270 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#2: Chemical	ChemComp-LRX / squarunkin A / ethyl 4-[[3,4-bis(oxidanylidene)-2-[2-[4-[3-(trifluoromethyl)phenyl]piperazin-1-yl]ethylamino]cyclobuten-1-yl]amino]piperidine-1-carboxylate Mass: 523.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₅H₃₂F₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#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.: 336 / 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: 2.61 Å³/Da / Density % sol: 52.93 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% w/v PEG3350 100 mM Sodium acetate pH 4.6 200-mM ammonium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.21→74.395 Å / Num. obs: 61768 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.998 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.21→2.27 Å / Num. unique obs: 4463 / CC_1/2: 0.626

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.21→74.395 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.929 / SU B: 8.31 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.223
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2574	3200	5.187 %
R_work	0.2223	58492	-
all	0.224	-	-
obs	-	61692	99.947 %

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: 44.522 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.396 Å²	0 Å²	0 Å²
2-	-	1.474 Å²	-0 Å²
3-	-	-	-2.87 Å²

Refinement step

Cycle: LAST / Resolution: 2.21→74.395 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8162	0	82	336	8580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	8571
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7814
X-RAY DIFFRACTION	r_angle_refined_deg	0.727	1.832	11580
X-RAY DIFFRACTION	r_angle_other_deg	0.289	1.777	18036
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.532	5	997
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.977	5	67
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.297	10	1411
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.811	10	458
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	1181
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10110
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	2190
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	1385
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	7023
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	3953
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4429
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	366
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.044	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.096	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.085	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	3.537	4.365	3973
X-RAY DIFFRACTION	r_mcbond_other	3.533	4.364	3972
X-RAY DIFFRACTION	r_mcangle_it	5.258	7.815	4963
X-RAY DIFFRACTION	r_mcangle_other	5.257	7.815	4964
X-RAY DIFFRACTION	r_scbond_it	4.036	4.823	4598
X-RAY DIFFRACTION	r_scbond_other	4.035	4.823	4596
X-RAY DIFFRACTION	r_scangle_it	6.388	8.675	6609
X-RAY DIFFRACTION	r_scangle_other	6.387	8.675	6610
X-RAY DIFFRACTION	r_lrange_it	8.651	43.936	9068
X-RAY DIFFRACTION	r_lrange_other	8.648	43.461	9032
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.104	0.05	5085
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.109	0.05	5066
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.106	0.05	5110
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.089	0.05	5138
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.126	0.05	4981
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.103	0.05	5337
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.088	0.05	5449
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.104	0.05	5267
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.11	0.05	5207
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.093	0.05	5174
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.103	0.05	5082
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.112	0.05	5099
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.103	0.05	5107
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.113	0.05	5089
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.121	0.05	4884

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	D	X-RAY DIFFRACTION	Local ncs	0.10353	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10353	0.05009
2	3	D	X-RAY DIFFRACTION	Local ncs	0.10886	0.05009
2	4	B	X-RAY DIFFRACTION	Local ncs	0.10886	0.05009
3	5	D	X-RAY DIFFRACTION	Local ncs	0.10612	0.05009
3	6	C	X-RAY DIFFRACTION	Local ncs	0.10612	0.05009
4	7	D	X-RAY DIFFRACTION	Local ncs	0.08858	0.0501
4	8	E	X-RAY DIFFRACTION	Local ncs	0.08858	0.0501
5	9	D	X-RAY DIFFRACTION	Local ncs	0.12588	0.05009
5	10	K	X-RAY DIFFRACTION	Local ncs	0.12588	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.1035	0.0501
6	12	B	X-RAY DIFFRACTION	Local ncs	0.1035	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08801	0.0501
7	14	C	X-RAY DIFFRACTION	Local ncs	0.08801	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.10376	0.0501
8	16	E	X-RAY DIFFRACTION	Local ncs	0.10376	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.11047	0.0501
9	18	K	X-RAY DIFFRACTION	Local ncs	0.11047	0.0501
10	19	B	X-RAY DIFFRACTION	Local ncs	0.09293	0.0501
10	20	C	X-RAY DIFFRACTION	Local ncs	0.09293	0.0501
11	21	B	X-RAY DIFFRACTION	Local ncs	0.10291	0.05009
11	22	E	X-RAY DIFFRACTION	Local ncs	0.10291	0.05009
12	23	B	X-RAY DIFFRACTION	Local ncs	0.11187	0.0501
12	24	K	X-RAY DIFFRACTION	Local ncs	0.11187	0.0501
13	25	C	X-RAY DIFFRACTION	Local ncs	0.10322	0.0501
13	26	E	X-RAY DIFFRACTION	Local ncs	0.10322	0.0501
14	27	C	X-RAY DIFFRACTION	Local ncs	0.11261	0.0501
14	28	K	X-RAY DIFFRACTION	Local ncs	0.11261	0.0501
15	29	E	X-RAY DIFFRACTION	Local ncs	0.1212	0.05009
15	30	K	X-RAY DIFFRACTION	Local ncs	0.1212	0.05009

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
2.21-2.267	0.368	241	0.335	4212	0.337	4455	0.887	0.905	99.9551	0.322
2.267-2.329	0.321	242	0.324	4157	0.323	4401	0.91	0.913	99.9546	0.307
2.329-2.397	0.343	208	0.3	4064	0.302	4273	0.918	0.929	99.9766	0.281
2.397-2.471	0.322	206	0.297	3945	0.299	4162	0.929	0.936	99.7357	0.273
2.471-2.552	0.332	216	0.289	3825	0.292	4042	0.933	0.944	99.9753	0.262
2.552-2.641	0.316	206	0.26	3687	0.263	3893	0.937	0.956	100	0.229
2.641-2.741	0.292	192	0.241	3552	0.244	3744	0.943	0.963	100	0.209
2.741-2.852	0.319	178	0.233	3453	0.237	3631	0.943	0.965	100	0.2
2.852-2.979	0.285	166	0.221	3337	0.224	3505	0.946	0.969	99.9429	0.191
2.979-3.124	0.268	192	0.21	3160	0.213	3352	0.953	0.972	100	0.182
3.124-3.293	0.249	138	0.206	3032	0.208	3171	0.959	0.973	99.9685	0.183
3.293-3.492	0.251	168	0.207	2856	0.21	3024	0.966	0.975	100	0.189
3.492-3.733	0.231	153	0.2	2694	0.202	2849	0.968	0.979	99.9298	0.186
3.733-4.031	0.217	136	0.201	2542	0.202	2678	0.973	0.978	100	0.188
4.031-4.414	0.206	132	0.184	2311	0.185	2444	0.975	0.981	99.9591	0.18
4.414-4.933	0.198	99	0.17	2142	0.171	2242	0.977	0.983	99.9554	0.167
4.933-5.692	0.232	110	0.186	1876	0.188	1986	0.972	0.982	100	0.182
5.692-6.961	0.232	87	0.209	1612	0.21	1699	0.973	0.977	100	0.203
6.961-9.802	0.279	86	0.216	1272	0.22	1359	0.956	0.974	99.9264	0.222
9.802-74.395	0.239	44	0.29	763	0.287	814	0.97	0.943	99.14	0.314

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