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- PDB-8vjv: Structure of Human Neurolysin in complex with dynorphin A8(1-8) p... -

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Basic information

Entry
Database: PDB / ID: 8vjv
TitleStructure of Human Neurolysin in complex with dynorphin A8(1-8) peptide
Components
  • Dynorphin A(1-8)
  • Neurolysin, mitochondrial
KeywordsHYDROLASE / metallopeptidase / bioactive peptides
Function / homology
Function and homology information


neurolysin / regulation of skeletal muscle fiber differentiation / opioid peptide activity / Opioid Signalling / peptide metabolic process / sensory perception / regulation of gluconeogenesis / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus ...neurolysin / regulation of skeletal muscle fiber differentiation / opioid peptide activity / Opioid Signalling / peptide metabolic process / sensory perception / regulation of gluconeogenesis / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus / peptide binding / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / metalloendopeptidase activity / mitochondrial intermembrane space / G-protein activation / G alpha (i) signalling events / chemical synaptic transmission / G protein-coupled receptor signaling pathway / neuronal cell body / dendrite / mitochondrion / 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: 2.12 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
D: Dynorphin A(1-8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8837
Polymers77,5962
Non-polymers2875
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-43 kcal/mol
Surface area27000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.168, 60.116, 95.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#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(1-8)


Mass: 983.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01213

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Non-polymers , 4 types, 83 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
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: 0.97912 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: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.12→95.734 Å / Num. obs: 42142 / % possible obs: 88.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 44.84 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.047 / Rrim(I) all: 0.146 / Net I/σ(I): 10.3
Reflection shellResolution: 2.123→2.244 Å / % possible obs: 29.2 % / Redundancy: 9.2 % / Rmerge(I) obs: 2.326 / Num. measured all: 19296 / Num. unique obs: 2090 / Rpim(I) all: 0.798 / Rrim(I) all: 2.462 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→95.73 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 2075 4.92 %
Rwork0.2131 40060 -
obs0.2148 42135 88.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.11 Å2
Refinement stepCycle: LAST / Resolution: 2.12→95.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 14 78 5505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00135553
X-RAY DIFFRACTIONf_angle_d0.39977479
X-RAY DIFFRACTIONf_chiral_restr0.0357812
X-RAY DIFFRACTIONf_plane_restr0.0034962
X-RAY DIFFRACTIONf_dihedral_angle_d11.01162098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.2806160.3024236X-RAY DIFFRACTION8.1
2.17-2.230.3635640.30911137X-RAY DIFFRACTION38.42
2.23-2.290.34031310.31032514X-RAY DIFFRACTION85.32
2.29-2.350.34491690.30342879X-RAY DIFFRACTION97.72
2.35-2.430.31991600.28452966X-RAY DIFFRACTION99.87
2.43-2.520.31341450.27732990X-RAY DIFFRACTION100
2.52-2.620.2841410.26082989X-RAY DIFFRACTION99.97
2.62-2.740.27071660.25652982X-RAY DIFFRACTION100
2.74-2.880.30781770.26092965X-RAY DIFFRACTION100
2.88-3.060.30131490.28592992X-RAY DIFFRACTION99.87
3.06-3.30.31071670.26253001X-RAY DIFFRACTION99.72
3.3-3.630.28081510.21933007X-RAY DIFFRACTION99.91
3.63-4.160.20111450.18483068X-RAY DIFFRACTION99.94
4.16-5.240.20141490.15163083X-RAY DIFFRACTION99.91
5.24-95.730.17721450.1643251X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 32.2676711611 Å / Origin y: 20.4288545976 Å / Origin z: 21.9531939088 Å
111213212223313233
T0.328098295817 Å2-0.0385271073213 Å20.0107298123101 Å2-0.325649715639 Å2-0.02060884951 Å2--0.314385106766 Å2
L1.19094120262 °2-0.352376634302 °20.232493521637 °2-1.0739660739 °2-0.142065350117 °2--0.503715165814 °2
S0.0568927025675 Å °0.0582411895499 Å °-0.053238970237 Å °0.114359127098 Å °-0.090488979684 Å °-0.0094088443435 Å °-0.00289456456801 Å °-0.0201188346677 Å °0.029636661172 Å °
Refinement TLS groupSelection details: all

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