PDB-8vjy: Structure of Human Neurolysin in complex with Neurotensin peptide

ID or keywords:

Entry

Database: PDB / ID: 8vjy

Title

Structure of Human Neurolysin in complex with Neurotensin peptide

Components

Neurolysin, mitochondrial
Neurotensin

Keywords

HYDROLASE / metallopeptidase / bioactive peptides

Function / homology

Function and homology information

neurolysin / regulation of skeletal muscle fiber differentiation / peptide metabolic process / regulation of gluconeogenesis / Peptide ligand-binding receptors / peptide binding / mitochondrial intermembrane space / metalloendopeptidase activity / G protein-coupled receptor signaling pathway / proteolysis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Shi, K. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	R01NS106879	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM118047	United States

Citation

Journal: Sci Rep / Year: 2024
Title: Structural basis of divergent substrate recognition and inhibition of human neurolysin.
Authors: Shi, K. / Bagchi, S. / Bickel, J. / Esfahani, S.H. / Yin, L. / Cheng, T. / Karamyan, V.T. / Aihara, H.

History

Deposition	Jan 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8vjy.cif.gz	583.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8vjy.ent.gz	477.1 KB	Display	PDB format
PDBx/mmJSON format	8vjy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/8vjy ftp://data.pdbj.org/pub/pdb/validation_reports/vj/8vjy	HTTPS FTP

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Related structure data

Related structure data	8vjuC 8vjvC 8vjxC 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	#28 - Apr 2002 Anthrax Toxin similarity (1) #217 - Jan 2018 Opioid Receptors similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #25 - Jan 2002 Thrombin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #149 - May 2012 Leptin similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: Neurolysin, mitochondrial

B: Neurotensin

C: Neurolysin, mitochondrial

D: Neurotensin

hetero molecules

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

1

A: Neurolysin, mitochondrial

B: Neurotensin

hetero molecules

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

2

C: Neurolysin, mitochondrial

D: Neurotensin

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.712, 150.576, 188.799
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Neurolysin, mitochondrial / Angiotensin-binding protein / Microsomal endopeptidase / MEP / Mitochondrial oligopeptidase M / ...Angiotensin-binding protein / Microsomal endopeptidase / MEP / Mitochondrial oligopeptidase M / Neurotensin endopeptidase Mass: 76688.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLN, AGTBP, KIAA1226 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYT8, neurolysin
#2: Protein/peptide	Neurotensin Mass: 1790.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.71 Å³/Da / Density % sol: 54.55 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.51 Å / Num. obs: 123468 / % possible obs: 99 % / Redundancy: 6.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.166 / R_pim(I) all: 0.071 / R_rim(I) all: 0.181 / Χ²: 1.83 / Net I/σ(I): 9.3 / Num. measured all: 783426
Reflection shell	Resolution: 1.95→1.98 Å / % possible obs: 80.8 % / Redundancy: 4.3 % / R_merge(I) obs: 2.914 / Num. measured all: 21292 / Num. unique obs: 4926 / CC_1/2: 0.157 / R_pim(I) all: 1.471 / R_rim(I) all: 3.286 / Χ²: 0.93 / Net I/σ(I) obs: 0.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
STARANISO		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→48.51 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2338	6091	4.94 %
R_work	0.1976	-	-
obs	0.1994	123328	98.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→48.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10856	0	90	995	11941

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	14.108	4302
X-RAY DIFFRACTION	f_chiral_restr	0.04	1651
X-RAY DIFFRACTION	f_plane_restr	0.005	1966

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 (%)
1.95-1.97	0.4528	146	0.413	2789	X-RAY DIFFRACTION	71
1.97-2	0.3729	212	0.375	3883	X-RAY DIFFRACTION	100
2-2.02	0.3547	203	0.349	3875	X-RAY DIFFRACTION	100
2.02-2.05	0.3685	210	0.3437	3931	X-RAY DIFFRACTION	100
2.05-2.07	0.332	208	0.3276	3878	X-RAY DIFFRACTION	100
2.07-2.1	0.3503	208	0.3177	3863	X-RAY DIFFRACTION	100
2.1-2.13	0.3524	191	0.2935	3991	X-RAY DIFFRACTION	100
2.13-2.16	0.3124	227	0.278	3839	X-RAY DIFFRACTION	100
2.16-2.2	0.3059	222	0.2749	3887	X-RAY DIFFRACTION	100
2.2-2.23	0.3214	192	0.2673	3912	X-RAY DIFFRACTION	100
2.23-2.27	0.3289	198	0.2558	3920	X-RAY DIFFRACTION	100
2.27-2.31	0.276	183	0.2327	3968	X-RAY DIFFRACTION	100
2.31-2.36	0.2455	178	0.2201	3907	X-RAY DIFFRACTION	100
2.36-2.41	0.2411	205	0.2128	3928	X-RAY DIFFRACTION	100
2.41-2.46	0.2497	199	0.2128	3908	X-RAY DIFFRACTION	100
2.46-2.52	0.2685	205	0.2108	3946	X-RAY DIFFRACTION	100
2.52-2.58	0.239	217	0.2008	3906	X-RAY DIFFRACTION	100
2.58-2.65	0.2557	208	0.1938	3917	X-RAY DIFFRACTION	100
2.65-2.73	0.2444	203	0.1995	3944	X-RAY DIFFRACTION	100
2.73-2.81	0.2748	212	0.2135	3920	X-RAY DIFFRACTION	100
2.81-2.91	0.2575	169	0.2197	3974	X-RAY DIFFRACTION	100
2.91-3.03	0.261	222	0.2016	3943	X-RAY DIFFRACTION	100
3.03-3.17	0.239	185	0.1996	3990	X-RAY DIFFRACTION	100
3.17-3.34	0.2543	214	0.1943	3954	X-RAY DIFFRACTION	100
3.34-3.55	0.2172	217	0.186	3976	X-RAY DIFFRACTION	100
3.55-3.82	0.2158	194	0.162	3959	X-RAY DIFFRACTION	100
3.82-4.2	0.1718	178	0.1448	4042	X-RAY DIFFRACTION	100
4.2-4.81	0.1579	209	0.1333	4034	X-RAY DIFFRACTION	100
4.81-6.06	0.2028	231	0.1586	4059	X-RAY DIFFRACTION	100
6.06-48.51	0.1691	245	0.1605	4194	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	2.0294	0.6373	0.4952	0.6957	0.0509	2.1874	0.007	-0.1608	0.2905	0.0512	0.0003	-0.0862	-0.1091	0.2687	-0.0107	0.1706	0.0214	0.01	0.2334	-0.0642	0.3183	2.5444	-38.253	-18.0886
2	1.3994	0.4609	0.126	1.0747	0.3098	0.5685	-0.2087	0.2043	-0.2543	-0.2784	0.1708	-0.0487	0.1373	0.0879	0.0247	0.3771	0.0032	0.0552	0.2447	-0.0227	0.2675	-2.3742	-68.3465	-34.5797
3	1.4769	0.5963	0.5965	2.1222	0.8375	1.3642	-0.1308	0.0644	0.0973	-0.2136	0.0691	0.0442	-0.0299	0.0018	0.0878	0.203	0.0007	0.013	0.1891	0.0104	0.1972	-17.546	-48.9362	-28.3153
4	1.0869	0.053	0.1281	0.8808	0.7573	1.1602	-0.1154	-0.1622	-0.2298	0.0647	0.1044	-0.0133	0.214	0.0604	-0.0173	0.302	0.0383	0.0287	0.2298	0.042	0.3008	-9.4732	-66.0146	-19.7674
5	5.0015	-1.2436	-1.4093	4.1952	-3.3778	9.7293	0.1538	0.9988	-0.6476	0.9974	-0.4679	-0.2712	0.3167	-0.0937	0.2379	0.9953	0.1274	0.0186	0.8171	-0.1264	0.9659	-4.0929	-61.6729	-27.2928
6	2.027	-0.6939	-0.4731	1.5806	0.4536	2.2947	-0.1284	0.3786	-0.4162	-0.1939	0.137	-0.0776	0.1975	0.115	-0.0072	0.3283	-0.0556	0.0328	0.363	-0.1413	0.3774	32.234	-67.1284	-75.2517
7	2.1147	-1.1086	-0.6119	1.642	1.2203	0.9258	-0.3871	-0.1693	0.0266	0.3808	0.2935	-0.1482	0.2002	0.1204	0.0853	0.4617	-0.0056	-0.0221	0.2749	0.0109	0.2711	32.9794	-42.9841	-57.0414
8	1.8767	0.1394	-0.1377	2.7378	0.5122	0.798	-0.1564	0.1816	0.2761	0.0637	0.1317	0.0771	-0.1685	-0.0006	0.0244	0.2674	0.0079	-0.0504	0.2424	0.0547	0.1678	15.2867	-36.4741	-64.1188
9	2.1494	-1.1441	-1.0434	2.5568	1.4335	1.6009	-0.134	0.2	-0.0703	-0.1173	0.2024	-0.0558	0.0974	0.1635	-0.096	0.2073	-0.0253	-0.0149	0.3229	-0.0274	0.2127	15.7247	-49.4168	-69.3301
10	1.8699	-0.1627	-0.2604	0.7972	0.5249	1.0086	-0.1032	0.4586	0.2343	-0.1808	0.132	-0.0121	-0.1303	-0.0373	-0.0217	0.4252	-0.0647	0.0062	0.3508	0.0695	0.3085	21.8406	-36.5479	-74.3147
11	5.3567	-4.0504	-0.1946	3.1257	-0.2111	2.0445	0.1425	-0.4948	0.1458	-0.2695	0.1173	-0.5088	0.0885	-0.0119	-0.3787	1.2215	-0.1686	-0.1239	0.9477	-0.0978	1.2826	25.3293	-43.5107	-66.9785

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 158 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 159 through 378 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 379 through 465 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 466 through 679 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 7 through 13 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 15 through 158 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 159 through 288 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 289 through 415 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 416 through 521 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 522 through 679 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 7 through 13 )

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