PDB-3noi: Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NK...

ID or keywords:

Entry

Database: PDB / ID: 3noi

Title

Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKp30 (NCR3)

Components

Natural cytotoxicity triggering receptor 3

Keywords

IMMUNE SYSTEM / Innate immunity / Immunoglobulin-like I2 type domain / Natural Killer cell activation / Natural Killer cells

Function / homology

Function and homology information

cell recognition / immune response-activating cell surface receptor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inflammatory response / immune response / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.842 Å

Authors

Joyce, M.G. / Sun, P.D.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the Natural Killer cell activating receptor NKp30 and dissection of ligand binding site
Authors: Joyce, M.G. / Tran, P. / Zhuravleva, M.A. / Jaw, J. / Colonna, M. / Sun, P.D.

History

Deposition	Jun 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3noi.cif.gz	160.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3noi_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3noi_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3noi_validation.xml.gz	14.1 KB	Display
Data in CIF	3noi_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/no/3noi ftp://data.pdbj.org/pub/pdb/validation_reports/no/3noi	HTTPS FTP

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Related structure data

Similar structure data	1ml9-d 6alw-2 6a9a-d 3r6g-1 4j97-3 4fz7-d 5neb-1 2gtk-d 6jq7-d 5ecw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

A: Natural cytotoxicity triggering receptor 3

B: Natural cytotoxicity triggering receptor 3

hetero molecules

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

1

A: Natural cytotoxicity triggering receptor 3

hetero molecules

B: Natural cytotoxicity triggering receptor 3

hetero molecules

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	45.100, 53.020, 51.952
Angle α, β, γ (deg.)	90.00, 107.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Natural cytotoxicity triggering receptor 3 / Natural killer cell p30-related protein / Activating natural killer receptor p30 Mass: 13248.904 Da / Num. of mol.: 2 / Fragment: Extracellular domain (unp residues 18-130) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NKp30, 1C7, LY117, NCR3 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 star / References: UniProt: O14931
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL Mass: 252.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₂₄O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.6 ul of mother liquor containing 40% PEG 200, 1.4% PEG400, 10 mM CaCl2, 50 mM HEPES pH 7.4 to 2 ul of protein followed by addition of 0.4 ul of 0.1 M EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.79→50 Å / Num. obs: 19666 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / B_iso Wilson estimate: 36 Å² / R_merge(I) obs: 0.105 / R_sym value: 0.105 / Net I/σ(I): 150.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
BALBES	+ EPMR	phasing
PHENIX	(phenix.refine: 1.6_289)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.842→38.815 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.204	1006	5.12 %
R_work	0.1642	-	-
obs	0.1664	19660	96.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 73.551 Å² / k_sol: 0.458 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.6295 Å²	0 Å²	0.1114 Å²
2-	-	-0.4172 Å²	0 Å²
3-	-	-	-0.2122 Å²

Refinement step

Cycle: LAST / Resolution: 1.842→38.815 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1847	0	44	135	2026

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2060
X-RAY DIFFRACTION	f_angle_d	1.346	2812
X-RAY DIFFRACTION	f_dihedral_angle_d	18.102	794
X-RAY DIFFRACTION	f_chiral_restr	0.096	310
X-RAY DIFFRACTION	f_plane_restr	0.006	371

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 (%)
1.8418-1.9389	0.2748	125	0.216	2441	X-RAY DIFFRACTION	89
1.9389-2.0604	0.2612	121	0.1874	2684	X-RAY DIFFRACTION	97
2.0604-2.2194	0.217	136	0.1646	2668	X-RAY DIFFRACTION	97
2.2194-2.4427	0.1992	144	0.1604	2663	X-RAY DIFFRACTION	98
2.4427-2.7961	0.2318	139	0.1598	2722	X-RAY DIFFRACTION	98
2.7961-3.5225	0.2008	171	0.144	2696	X-RAY DIFFRACTION	99
3.5225-38.824	0.183	170	0.1654	2780	X-RAY DIFFRACTION	99

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	0.416	0.5786	-0.2155	1.236	0.1072	0.4866	0.1238	0.0792	0.3566	0.399	-0.0308	-1.4403	0.355	0.6608	-0.0386	0.3739	0.1491	0.1619	0.3811	-0.0354	0.8498	14.6636	12.3872	20.8612
2	0.0872	-0.1414	0.0616	0.2784	-0.2058	0.2021	-1.0244	0.3383	0.3775	0.8388	0.2689	0.9572	-0.8334	-0.0761	-0.0054	0.2521	0.0383	-0.0421	0.2419	-0.0539	0.3909	26.1503	9.5801	27.7423
3	0.1105	-0.0591	0.0457	0.314	-0.2706	0.3485	0.407	0.1066	0.8118	-0.2328	0.1633	-0.2451	-0.5937	0.2862	0.0004	0.2606	-0.0355	-0.0137	0.2545	-0.0118	0.2463	40.8732	5.6857	19.5591
4	1.0117	-0.2597	-1.3612	4.4871	4.4627	6.4592	0.7485	0.2185	0.7425	-2.2444	-0.7389	-0.9942	-2.4849	0.125	0.1266	0.3679	0.0058	0.0509	0.3589	-0.011	0.2068	49.4305	-3.2074	10.4822
5	7.7016	-1.664	4.7628	4.8585	-5.0685	6.5965	-0.0351	-1.6438	0.2666	1.0216	0.273	-0.0966	-0.7592	-0.568	0.197	-0.0083	-0.1678	-0.029	-0.0043	0.0391	0.2369	43.6977	-5.6981	16.1481
6	0.0405	-0.0286	-0.0346	0.0396	-0.0604	0.0782	0.2885	0.191	0.2597	-0.4231	-0.1135	-0.1701	-1.0697	0.2708	-0.0003	0.2277	-0.0045	0.012	0.2295	0.0036	0.2307	33.6617	2.2373	26.9321
7	0.1812	0.1262	-0.2155	0.0507	-0.1309	0.2431	0.2441	-0.155	0.0433	0.1873	-0.106	0.6621	0.0894	-0.4159	-0.0006	0.2495	-0.0259	0.0376	0.2808	0.0076	0.3444	27.3657	-2.4179	34.8419
8	0.0142	0.0565	-0.0809	0.095	-0.1525	0.1569	-0.0072	0.3122	-0.1849	-0.4182	0.1532	0.3974	-0.1128	-0.7328	0.0001	0.2514	-0.0453	-0.0176	0.2403	-0.0117	0.2084	28.5306	0.0866	17.2443
9	0.2699	0.0256	0.392	0.019	0.0144	0.4982	-0.0206	0.7197	1.5471	-0.9075	-0.1494	0.047	-0.0693	-0.1827	-0.003	0.3212	-0.0377	-0.0876	0.3867	0.0346	0.4803	30.0082	6.1038	7.6295
10	2.6301	-0.7627	1.6805	0.9491	-0.3194	1.1231	0.2309	0.65	-0.1706	-0.4857	0.4646	1.8913	0.2633	-0.3734	0.0406	0.4827	0.0084	-0.1757	0.2845	0.0129	0.5143	27.7307	-1.5838	8.3729
11	0.3059	0.0243	0.3095	0.443	0.2653	0.463	0.4757	1.8689	1.2907	0.0301	0.6428	0.4784	-0.7392	-0.3446	0.024	0.3534	0.0375	-0.0438	0.5753	0.1208	0.3733	32.0874	-6.948	5.4828
12	0.5486	0.1529	0.3007	0.1804	0.01	0.1659	0.0263	-0.6129	-0.153	0.4249	0.1134	0.3153	0.5308	-0.2156	0.0047	0.2157	-0.0842	-0.0595	0.1969	0.0249	0.2187	34.7692	-11.3462	6.6129
13	0.8596	-0.1456	-0.1346	0.4005	0.4507	0.4531	-0.273	-0.0448	-0.2092	-0.042	0.2802	-0.3396	0.3214	0.0238	-0.0006	0.2871	-0.0012	0.023	0.2284	0.0056	0.2654	31.7234	-6.935	27.1419
14	0.0688	-0.0523	-0.0995	0.0598	0.0737	0.1199	0.0822	-0.1895	0.196	0.3598	0.0558	-0.3575	-0.8201	0.5623	0.0001	0.2361	-0.0341	0.0137	0.2655	0.0577	0.314	37.5398	-5.4319	17.364
15	0.1464	-0.1572	0.0865	0.996	-0.5707	0.2853	0.2076	0.02	-0.763	-1.0271	-0.1082	-0.1824	1.3736	-0.4445	0.0265	0.4876	-0.145	-0.0207	0.4162	-0.0111	0.2322	43.2577	-8.4958	7.7263
16	0.6517	-0.9217	0.2609	1.3555	-0.5686	0.3286	-0.1409	0.023	-0.2958	-0.4631	-0.0013	0.6793	-0.0135	0.1576	0.0007	0.2886	-0.004	-0.021	0.2741	0.0537	0.1804	38.1726	2.0598	9.522
17	0.6927	-0.2931	0.2736	0.5318	-0.5136	0.4387	0.1373	-0.1161	0.0494	-0.2974	-0.118	-0.2121	-0.6885	0.1886	0.0008	0.2466	0.0103	0.0039	0.2135	-0.0335	0.3129	23.2401	3.0629	24.758
18	0.2341	-0.4319	0.2218	0.6222	-0.4219	0.2095	-0.1645	0.6253	0.3017	-0.2147	0.2031	0.0182	-0.0063	-0.1446	-0.0033	0.2289	-0.0437	-0.0168	0.2153	0.0103	0.2589	35.4872	7.9914	17.6079
19	0.7431	-0.1838	-0.2885	0.8515	0.0423	0.9188	-0.0716	0.8874	-0.3449	-1.026	0.0458	0.2107	-0.2533	-0.6706	0.0127	0.3231	-0.0276	0.1244	0.2399	0.019	0.2275	49.8974	-0.2423	8.4814
20	0.0777	0.034	-0.0111	0.0211	-0.0934	0.3079	-0.125	0.058	-0.2633	0.4109	0.3643	0.1532	0.0014	0.399	-0.018	0.3253	0.1191	-0.0993	0.271	0.0345	0.4338	5.762	19.8188	28.9733
21	1.294	1.0572	0.4513	3.4575	1.4541	0.7938	-0.5821	0.3333	-0.3397	-2.1794	0.2905	1.2294	-0.041	-1.0409	-0.0365	0.4491	-0.0422	-0.0214	0.3183	-0.0217	0.2085	7.7469	10.2276	19.7729
22	0.2949	-0.197	0.4279	0.1361	-0.2573	0.5875	0.4401	0.4453	0.636	-0.348	-0.1753	-0.2949	-0.8102	0.0459	0.0021	0.189	0.023	0.0171	0.1685	0.0052	0.157	-3.3516	7.6853	29.3757
23	0.6233	-0.2793	-0.285	0.2476	0.0778	0.2453	-0.1455	-0.1003	-0.0495	1.069	0.0931	-0.2022	-0.8299	-0.6696	-0.0076	0.3161	-0.0092	0.0343	0.3238	0.0312	0.2133	-11.6692	2.5223	39.8264
24	0.2474	-0.3272	0.2696	0.9333	-0.1941	0.2885	0.262	0.015	0.2151	0.0722	0.1244	-0.0158	0.2242	-0.1686	0.0008	0.2859	-0.0342	-0.0347	0.3069	-0.0268	0.2364	-4.3124	-1.0561	34.9322
25	0.2528	0.2219	0.3218	0.1939	0.3359	0.5371	0.4035	0.6529	0.506	-0.3339	-0.0625	-0.4575	-0.1153	-0.2812	-0.005	0.2871	0.0071	0.0237	0.326	0.0047	0.2653	6.6802	-1.0929	17.8285
26	0.2467	-0.1141	-0.0233	0.4728	-0.4589	0.4642	-0.1837	0.4743	-0.5558	-0.4104	-0.1781	-0.3913	0.2791	0.1922	0.003	0.2575	0.055	0.0553	0.2901	-0.0141	0.2923	11.9307	-3.0936	26.5969
27	6.7525	-4.4782	-2.5572	3.5427	1.2694	1.5344	0.026	-1.3084	1.1384	0.5495	0.3071	-1.1898	-0.1017	0.7902	0.1904	0.2185	-0.0665	-0.0182	0.3057	-0.0352	0.268	5.5153	8.3486	38.3246
28	2.0006	5.0216	-8.5245	7.2554	-1.5975	7.5085	-0.5257	-1.0337	-0.688	0.9145	-0.2881	-1.5434	1.0327	1.7742	-0.3695	0.2327	-0.1343	-0.0945	0.464	-0.0347	0.3661	9.7466	8.6531	41.9784
29	2.7162	0.6538	1.7878	0.3678	0.4628	1.3473	0.1686	-0.5516	0.6485	-0.6573	-0.8027	-0.2435	-0.7874	-0.6214	-0.0519	0.4738	-0.0205	-0.0825	0.4396	0.0376	0.6688	5.8235	1.0941	48.8268
30	3.0641	-0.2831	0.3958	0.7906	0.9373	7.2162	0.3942	-0.5345	-1.0991	0.9025	-0.0959	-0.8806	1.5422	0.6011	-0.0774	0.2753	-0.0291	-0.0564	0.3683	0.0341	0.1677	1.1782	-3.0345	46.3497
31	0.1976	-0.0355	-0.0414	0.005	0.0083	0.0302	-0.4903	-0.6215	-1.1966	0.6248	0.1386	0.2767	0.8832	-0.2753	-0.0039	0.3755	0.0588	0.0212	0.35	0.0155	0.4836	4.7068	-8.6301	30.4866
32	0.1667	0.1012	-0.195	0.1193	-0.1763	0.4372	-0.148	0.0391	-0.8384	-0.0563	-0.2035	0.385	1.5	-0.4616	0.0011	0.2912	-0.03	0.0554	0.2175	-0.0273	0.3032	6.4941	-6.3636	23.5656
33	0.8119	1.3753	-1.8967	2.2344	-2.5416	8.7964	-0.3312	0.1862	-0.6071	-0.5852	0.071	-0.4149	1.241	0.0908	-0.1431	0.165	-0.0103	0.0119	0.1606	0.014	0.1563	-0.368	-3.3712	35.8882
34	0.2378	-0.1288	0.2585	0.1125	-0.0818	0.2538	0.4264	-0.1035	-0.4874	-1.1699	-0.1686	0.164	-0.5301	0.103	0.0003	0.3466	-0.0984	0.0142	0.3933	-0.0168	0.2004	-6.2276	0.836	48.0468
35	0.1316	0.1311	-0.1512	0.0865	-0.1754	0.2178	0.0403	-0.2152	0.243	0.3219	0.1074	-0.4774	0.1788	0.03	0.0018	0.2123	-0.0044	-0.0152	0.2692	-0.0218	0.1935	-0.6237	7.4633	39.2013
36	0.4177	0.3496	0.1402	0.2491	0.0974	0.0724	0.0747	-0.13	0.1498	0.461	0.1484	-0.7142	0.5419	0.0636	-0.0056	0.2313	-0.0088	0.0112	0.2605	-0.0161	0.3048	13.2134	3.8792	26.4999
37	1.0081	-0.4321	-0.8822	0.1024	0.2283	0.4666	0.3676	0.5081	1.3509	-0.0411	0.033	-0.4266	-0.4166	-0.0019	0.0106	0.1699	0.01	-0.0179	0.2563	0.0105	0.2687	2.0843	9.4495	30.9826
38	0.5409	-0.055	-0.582	0.875	0.1121	0.5894	0.3311	0.0938	-0.3928	0.5242	-0.541	1.4271	0.0234	-0.3388	-0.0123	0.3597	-0.0736	0.1498	0.3411	-0.055	0.4457	-13.7141	4.0521	42.5849

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 12:15)
2	X-RAY DIFFRACTION	2	(chain A and resid 16:20)
3	X-RAY DIFFRACTION	3	(chain A and resid 21:27)
4	X-RAY DIFFRACTION	4	(chain A and resid 28:32)
5	X-RAY DIFFRACTION	5	(chain A and resid 33:37)
6	X-RAY DIFFRACTION	6	(chain A and resid 38:43)
7	X-RAY DIFFRACTION	7	(chain A and resid 44:50)
8	X-RAY DIFFRACTION	8	(chain A and resid 51:56)
9	X-RAY DIFFRACTION	9	(chain A and resid 57:63)
10	X-RAY DIFFRACTION	10	(chain A and resid 64:67)
11	X-RAY DIFFRACTION	11	(chain A and resid 68:73)
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18	X-RAY DIFFRACTION	18	(chain A and resid 116:124)
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36	X-RAY DIFFRACTION	36	(chain B and resid 109:115)
37	X-RAY DIFFRACTION	37	(chain B and resid 116:124)
38	X-RAY DIFFRACTION	38	(chain B and resid 125:130)

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