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- PDB-8vju: Structure of Human Neurolysin in complex with dynorphin A13 peptide -

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Basic information

Entry
Database: PDB / ID: 8vju
TitleStructure of Human Neurolysin in complex with dynorphin A13 peptide
Components
  • Dynorphin A(1-13)
  • Neurolysin, mitochondrial
KeywordsHYDROLASE / metallopeptidase / bioactive peptides
Function / homology
Function and homology information


neurolysin / regulation of skeletal muscle fiber differentiation / opioid receptor binding / opioid peptide activity / Opioid Signalling / peptide metabolic process / sensory perception / regulation of gluconeogenesis / neuronal dense core vesicle / neuropeptide signaling pathway ...neurolysin / regulation of skeletal muscle fiber differentiation / opioid receptor binding / opioid peptide activity / Opioid Signalling / peptide metabolic process / sensory perception / regulation of gluconeogenesis / neuronal dense core vesicle / neuropeptide signaling pathway / axon terminus / hippocampal mossy fiber to CA3 synapse / Peptide ligand-binding receptors / peptide binding / G-protein activation / metalloendopeptidase activity / mitochondrial intermembrane space / G alpha (i) signalling events / chemical synaptic transmission / G protein-coupled receptor signaling pathway / neuronal cell body / dendrite / proteolysis / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Proenkephalin B / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature. / 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
Proenkephalin-B / Neurolysin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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

Downloads & links

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Assembly

Deposited unit
A: Neurolysin, mitochondrial
C: Dynorphin A(1-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,93015
Polymers78,2222
Non-polymers70913
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-77 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.067, 60.257, 95.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#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 Dynorphin A(1-13)


Mass: 1608.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01213

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Non-polymers , 5 types, 266 molecules

#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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.95 %
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-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.987→79.29 Å / Num. obs: 48708 / % possible obs: 84.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Rrim(I) all: 0.067 / Net I/σ(I): 9.7
Reflection shellResolution: 1.987→2.111 Å / % possible obs: 25.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.823 / Num. measured all: 7684 / Num. unique obs: 2435 / Rpim(I) all: 0.528 / Rrim(I) all: 0.981 / Net I/σ(I) obs: 1.4

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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: 1.99→79.29 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 2422 4.97 %
Rwork0.195 --
obs0.1962 48703 85.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→79.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5419 0 37 253 5709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d14.8182115
X-RAY DIFFRACTIONf_chiral_restr0.037817
X-RAY DIFFRACTIONf_plane_restr0.005964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.157100.3115176X-RAY DIFFRACTION6
2.03-2.070.41410.2988818X-RAY DIFFRACTION26
2.07-2.120.3116940.28121749X-RAY DIFFRACTION56
2.12-2.170.32011380.2642684X-RAY DIFFRACTION84
2.17-2.230.29561660.25842999X-RAY DIFFRACTION96
2.23-2.30.26971740.2393148X-RAY DIFFRACTION99
2.3-2.370.25721590.22953115X-RAY DIFFRACTION99
2.37-2.460.27611580.22523135X-RAY DIFFRACTION99
2.46-2.560.27441650.22993102X-RAY DIFFRACTION98
2.56-2.670.25361530.23013074X-RAY DIFFRACTION96
2.67-2.810.29531600.24453159X-RAY DIFFRACTION99
2.81-2.990.25181590.22883195X-RAY DIFFRACTION99
2.99-3.220.25651720.22183159X-RAY DIFFRACTION99
3.22-3.550.22921670.20133191X-RAY DIFFRACTION99
3.55-4.060.19921600.17223130X-RAY DIFFRACTION97
4.06-5.110.15761750.14433239X-RAY DIFFRACTION99
5.11-79.290.1571710.15963208X-RAY DIFFRACTION94
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)
11.479-0.4708-0.18782.0120.0521.88320.0453-0.09010.08780.1913-0.07640.3695-0.1728-0.26820.07740.297-0.01880.03780.3228-0.0420.4233-53.219718.0179-21.0713
21.5152-0.5088-0.30521.62150.21320.29690.12360.28030.1464-0.0884-0.1686-0.2676-0.07370.02230.02850.276-0.0185-0.01240.39450.06110.2643-21.339312.6125-33.7278
32.069-1.1221-0.45141.93290.52031.38170.0660.1079-0.2030.1829-0.10920.2230.1086-0.06620.06530.2666-0.043-0.00160.2125-0.00760.277-38.89760.0559-25.8215
40.7403-0.4949-0.34681.75120.24120.86220.0217-0.07310.04830.3487-0.039-0.16860.04180.06980.02050.3222-0.0523-0.080.31790.03350.2773-22.7296.1206-19.0175
58.1464-0.99862.26033.9061-3.62787.41540.2004-1.32750.0077-0.66890.01360.16390.22080.1455-0.29820.7709-0.1062-0.05770.97840.02190.7-30.031810.9516-27.7479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 378 )
3X-RAY DIFFRACTION3chain 'A' and (resid 379 through 513 )
4X-RAY DIFFRACTION4chain 'A' and (resid 514 through 679 )
5X-RAY DIFFRACTION5chain 'C' and (resid 4 through 9 )

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