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- PDB-8vjw: Structure of Human Neurolysin in complex with angiotensin I peptide -

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Basic information

Entry
Database: PDB / ID: 8vjw
TitleStructure of Human Neurolysin in complex with angiotensin I peptide
Components
  • Angiotensin-1 peptide C-terminal end
  • Angiotensin-1 peptide N-terminal end
  • Neurolysin, mitochondrial
KeywordsHYDROLASE / 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 / metalloendopeptidase activity / mitochondrial intermembrane space / G protein-coupled receptor signaling pathway / proteolysis ...neurolysin / regulation of skeletal muscle fiber differentiation / peptide metabolic process / regulation of gluconeogenesis / Peptide ligand-binding receptors / peptide binding / metalloendopeptidase activity / mitochondrial intermembrane space / G protein-coupled receptor signaling pathway / proteolysis / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase family M3 / Peptidase M3A/M3B / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Neurolysin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurolysin, mitochondrial
B: Neurolysin, mitochondrial
C: Angiotensin-1 peptide N-terminal end
D: Angiotensin-1 peptide C-terminal end
E: Angiotensin-1 peptide N-terminal end
F: Angiotensin-1 peptide C-terminal end
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9918
Polymers155,8606
Non-polymers1312
Water1448
1
A: Neurolysin, mitochondrial
C: Angiotensin-1 peptide N-terminal end
D: Angiotensin-1 peptide C-terminal end
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9954
Polymers77,9303
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-48 kcal/mol
Surface area27430 Å2
MethodPISA
2
B: Neurolysin, mitochondrial
E: Angiotensin-1 peptide N-terminal end
F: Angiotensin-1 peptide C-terminal end
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9954
Polymers77,9303
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-48 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.078, 60.584, 147.759
Angle α, β, γ (deg.)90.00, 106.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 76612.539 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 Angiotensin-1 peptide N-terminal end


Mass: 552.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide Angiotensin-1 peptide C-terminal end


Mass: 764.913 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe author states that the Angiotensin-1 peptides are hydrolyzed. The full length sequence is DRVYIHPFHL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.491→141.622 Å / Num. obs: 33506 / % possible obs: 55.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.106 / Rrim(I) all: 0.202 / Net I/σ(I): 5.6 / Num. measured all: 117633
Reflection shellResolution: 2.491→2.844 Å / % possible obs: 8.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.943 / Num. measured all: 7290 / Num. unique obs: 1675 / Rpim(I) all: 0.512 / Rrim(I) all: 1.075 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.491→66.99 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 1630 4.87 %
Rwork0.2374 --
obs0.2397 33493 55.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.491→66.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10828 0 2 8 10838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d10.0454172
X-RAY DIFFRACTIONf_chiral_restr0.0361630
X-RAY DIFFRACTIONf_plane_restr0.0031914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.491-2.560.066820.463732X-RAY DIFFRACTION1
2.57-2.650.4051110.3734240X-RAY DIFFRACTION5
2.65-2.740.4124160.3365493X-RAY DIFFRACTION10
2.74-2.850.3135460.3588929X-RAY DIFFRACTION20
2.85-2.980.4042920.34111745X-RAY DIFFRACTION37
2.98-3.140.37111270.31832466X-RAY DIFFRACTION52
3.14-3.340.34941840.30243197X-RAY DIFFRACTION67
3.34-3.590.35522200.28444032X-RAY DIFFRACTION84
3.59-3.950.32092610.25574359X-RAY DIFFRACTION92
3.95-4.530.2482580.21094731X-RAY DIFFRACTION98
4.53-5.70.2421990.20284809X-RAY DIFFRACTION98
5.7-66.990.20862140.18764830X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL11 (°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)
11.77430.2017-0.22541.032-0.21041.0072-0.00330.3810.1379-0.540.10910.4206-0.1623-0.0861-0.02060.4157-0.0482-0.20490.24270.05280.3117-21.33.513-21.207
20.37590.03140.05931.5736-0.40571.30610.0618-0.13080.14240.1632-0.1223-0.1138-0.07260.49950.06470.3389-0.0061-0.02350.3809-0.00030.2036-16.551-3.06315.109
31.8290.5829-0.14451.2572-1.03231.5999-0.02180.1947-0.0085-0.08670.0163-0.0437-0.15540.1248-0.01060.44930.0774-0.13660.0272-0.07220.2717-18.525-20.035-5.486
40.6895-0.0710.49612.167-0.69650.97280.0182-0.098-0.0228-0.28670.01180.617-0.0015-0.1602-0.02550.25210.0183-0.09770.1883-0.00990.2837-31.205-10.2353.723
51.805-0.5541-0.03562.4714-0.58631.96690.103-0.4554-0.2260.41160.03330.9810.2949-0.2985-0.02520.3351-0.03150.10170.27290.02420.476-50.691-33.72280.255
60.38580.1763-0.93121.6802-0.72152.07740.0873-0.2018-0.1421-0.1434-0.15090.12570.23240.42870.06040.27980.0721-0.08070.25580.00750.2762-31.923-33.23953.486
71.78310.2357-0.67440.768-1.48432.87550.1333-0.1210.00230.2276-0.24060.3431-0.5910.0848-0.14470.14320.05840.06890.0735-0.16650.4051-39.931-8.49565.128
80.9510.2313-0.922.4939-0.80771.43810.2672-0.1356-0.28190.1485-0.0240.45780.5013-0.1215-0.07310.06370.0811-0.07990.1244-0.07210.4512-42.715-19.33463.858
91.46290.1935-0.39011.1304-0.36211.09160.1020.1499-0.1468-0.3582-0.03070.6480.0603-0.0385-0.04030.31110.0696-0.15590.1854-0.05750.3601-43.976-22.92248.871
100.08950.0790.16771.03780.18710.3158-0.0650.4677-0.46030.00810.10190.00150.0154-0.2982-0.02040.41530.07370.23041.17970.21831.2749-21.035-5.331-3.329
117.1989-4.1577-5.56883.0463.22884.3078-0.5320.0595-0.7541-0.5174-0.81111.1475-0.8754-0.85060.87350.9306-0.0885-0.47190.55790.01560.8875-21.812-7.3626.593
127.1406-0.0937-3.38611.0130.67621.9999-0.4820.0402-0.60860.07110.0120.19610.29320.2140.2830.9499-0.49540.30481.47950.04670.7079-40.959-28.15162.026
134.29042.6299-5.95424.8531-0.23092.00020.38141.39571.4245-0.7699-0.1455-0.0816-1.73650.5232-0.39060.4266-0.10070.14220.58810.11680.4453-35.752-25.71653.659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 15:184 )A15 - 184
2X-RAY DIFFRACTION2( CHAIN A AND RESID 185:350 )A185 - 350
3X-RAY DIFFRACTION3( CHAIN A AND RESID 351:484 )A351 - 484
4X-RAY DIFFRACTION4( CHAIN A AND RESID 485:679 )A485 - 679
5X-RAY DIFFRACTION5( CHAIN B AND RESID 15:136 )B15 - 136
6X-RAY DIFFRACTION6( CHAIN B AND RESID 137:350 )B137 - 350
7X-RAY DIFFRACTION7( CHAIN B AND RESID 351:415 )B351 - 415
8X-RAY DIFFRACTION8( CHAIN B AND RESID 416:513 )B416 - 513
9X-RAY DIFFRACTION9( CHAIN B AND RESID 514:679 )B514 - 679
10X-RAY DIFFRACTION10( CHAIN C AND RESID 3:4 )C3 - 4
11X-RAY DIFFRACTION11( CHAIN C AND RESID 5:8 )C5 - 8
12X-RAY DIFFRACTION12( CHAIN E AND RESID 3:4 )E3 - 4
13X-RAY DIFFRACTION13( CHAIN E AND RESID 5:8 )E5 - 8

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