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8vju

Structure of Human Neurolysin in complex with dynorphin A13 peptide

Method: X-RAY DIFFRACTION Dmax: 87.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurolysin, mitochondrial

Homo sapiens

UniProt Q9BYT8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 38–704 Not recorded Dynorphin A(1-13) × 1 （P01213） ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5 Resolution 1.99 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8VJU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LUZ Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products Deposited 2016-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.268
5LUZ Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products Deposited 2016-09-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.268
5LV0 Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product Deposited 2016-09-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.260
5LV0 Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product Deposited 2016-09-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.260
8VJV Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide Deposited 2024-01-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.12 Å R-free 0.249
8VJW Structure of Human Neurolysin in complex with angiotensin I peptide Deposited 2024-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.49 Å R-free 0.286
8VJW Structure of Human Neurolysin in complex with angiotensin I peptide Deposited 2024-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.49 Å R-free 0.286
8VJX Structure of Human Neurolysin in complex with bradykinin peptide Deposited 2024-01-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.89 Å R-free 0.255
8VJY Structure of Human Neurolysin in complex with Neurotensin peptide Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.95 Å R-free 0.234
8VJY Structure of Human Neurolysin in complex with Neurotensin peptide Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 38–704（667 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.95 Å R-free 0.234

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEUL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–667； UniProt 38–704

Dynorphin A(1-13)

OrganismNot specified

UniProt P01213

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 207–219 Not recorded Neurolysin, mitochondrial × 1 （Q9BYT8） ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5 Resolution 1.99 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8VJU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N2F Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor Deposited 2015-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 207–219（13 aa） Fragment：residues 207-219
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；280 K；Pressure ambient
NMR sample composition 1 mM [U-15N-GFLI] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-15N-GFLIR; U-13C-R] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8F7W Gi bound kappa-opioid receptor in complex with dynorphin Deposited 2022-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 207–214（8 aa） Fragment：UNP residues 207-214
Not recorded CLR CHOLESTEROL × 3 PLM PALMITIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
8VJV Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide Deposited 2024-01-08 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 207–214（8 aa）
Not recorded ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.12 Å R-free 0.249
9CCE structure of DYNA_1b7 Deposited 2024-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300
Resolution 3.15 Å R-free 0.313
9CCE structure of DYNA_1b7 Deposited 2024-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300
Resolution 3.15 Å R-free 0.313
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME
Resolution 4.00 Å R-free 0.296
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME
Resolution 4.00 Å R-free 0.296
9L60 Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15 Deposited 2024-12-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 207–219（13 aa）
Not recorded CLR CHOLESTEROL × 2 A1D6C 9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDYN_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–13； UniProt 207–219

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8vju

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vju
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vju
Deposition date deposition_date2024-01-08
最后修订 last_revision2024-08-21
Structure title titleStructure of Human Neurolysin in complex with dynorphin A13 peptide
Keywords keywordsmetallopeptidase, bioactive peptides, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.25 Å
Radius of gyration Rg (electron density) rg_electron25.24 Å
Forward intensity I(0) i097015500.00
Molecular weight molecular_weight77870.0 kDa
Excluded volume excluded_volume97581 ų
Envelope volume envelope_volume115160 ų
Hydration-shell volume shell_volume36703 ų
Envelope diameter envelope_diameter93.1 Å
Shell Rg shell_rg33.71 Å
Envelope Rg envelope_rg25.29 Å
Shape Rg shape_rg25.22 Å
Total Rg total_rg26.16 Å
Total atoms total_atoms5456
Residues n_residues671
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.4 Å
Rg (real space) rg_real26.11 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real9.7020e+07
I(0) uncertainty (real space) i0_real_error1.3960e+06
Rg (reciprocal space) rg_reciprocal26.16 Å
I(0) (reciprocal space) i0_reciprocal97020000.0000
Solution quality estimate total_estimate0.8701
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5 Å
Skewness Skewness skewness0.247
Kurtosis Kurtosis kurtosis-0.219
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23680000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)