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- PDB-8vjx: Structure of Human Neurolysin in complex with bradykinin peptide -

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Basic information

Entry
Database: PDB / ID: 8vjx
TitleStructure of Human Neurolysin in complex with bradykinin peptide
Components
  • Bradykinin
  • Neurolysin, mitochondrial
KeywordsHYDROLASE / metallopeptidase / bioactive peptides
Function / homology
Function and homology information


neurolysin / regulation of skeletal muscle fiber differentiation / peptide metabolic process / negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / regulation of gluconeogenesis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen ...neurolysin / regulation of skeletal muscle fiber differentiation / peptide metabolic process / negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / regulation of gluconeogenesis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / peptide binding / negative regulation of proteolysis / Post-translational protein phosphorylation / vasodilation / hormone activity / mitochondrial intermembrane space / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Proteinase inhibitor I25, cystatin, conserved site ...Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Kininogen-1 / Neurolysin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurolysin, mitochondrial
C: Bradykinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7403
Polymers77,6752
Non-polymers651
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-50 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.826, 60.510, 96.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1119-

HOH

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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.: 1
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 Bradykinin / Kallidin I


Mass: 1062.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01042
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.52 %
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: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.884→96.56 Å / Num. obs: 15148 / % possible obs: 77 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.108 / Rrim(I) all: 0.299 / Net I/σ(I): 5.9
Reflection shellResolution: 2.884→3.13 Å / % possible obs: 18.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.894 / Num. measured all: 5746 / Num. unique obs: 758 / Rpim(I) all: 0.718 / Rrim(I) all: 2.029 / Net I/σ(I) obs: 1.3

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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: 2.89→96.56 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 769 5.08 %
Rwork0.2233 --
obs0.2249 15138 77.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→96.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 1 26 5432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d14.8012090
X-RAY DIFFRACTIONf_chiral_restr0.036813
X-RAY DIFFRACTIONf_plane_restr0.003959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.110.2828470.3497586X-RAY DIFFRACTION17
3.11-3.420.35561520.30692512X-RAY DIFFRACTION69
3.42-3.920.29131600.2553666X-RAY DIFFRACTION98
3.92-4.940.23461900.19523727X-RAY DIFFRACTION100
4.94-96.560.22262200.19523878X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -32.274 Å / Origin y: 9.6184 Å / Origin z: -26.1358 Å
111213212223313233
T0.2489 Å2-0.0409 Å2-0.0085 Å2-0.2642 Å20.0323 Å2--0.3052 Å2
L1.3369 °2-0.4042 °2-0.2438 °2-1.0052 °20.2016 °2--0.7909 °2
S0.0125 Å °0.0787 Å °0.0575 Å °0.1076 Å °-0.0501 Å °0.0435 Å °-0.068 Å °-0.0059 Å °0.0378 Å °
Refinement TLS groupSelection details: all

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