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- PDB-5luz: Structure of Human Neurolysin (E475Q) in complex with neurotensin... -

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Basic information

Entry
Database: PDB / ID: 5luz
TitleStructure of Human Neurolysin (E475Q) in complex with neurotensin peptide products
Components
  • Neurolysin, mitochondrial
  • PRO-ARG-ARG-PRO neurotensin fragment
KeywordsHYDROLASE / PROTEASE / MITOCHONDRIA / NEUROTENSIN
Function / homology
Function and homology information


neurolysin / regulation of skeletal muscle fiber differentiation / neuropeptide receptor binding / peptide metabolic process / neuropeptide hormone activity / regulation of gluconeogenesis / neuropeptide signaling pathway / axon terminus / transport vesicle / blood vessel diameter maintenance ...neurolysin / regulation of skeletal muscle fiber differentiation / neuropeptide receptor binding / peptide metabolic process / neuropeptide hormone activity / regulation of gluconeogenesis / neuropeptide signaling pathway / axon terminus / transport vesicle / blood vessel diameter maintenance / Peptide ligand-binding receptors / peptide binding / metalloendopeptidase activity / mitochondrial intermembrane space / positive regulation of NF-kappaB transcription factor activity / G alpha (q) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / G protein-coupled receptor signaling pathway / negative regulation of gene expression / intracellular membrane-bounded organelle / positive regulation of gene expression / signal transduction / proteolysis / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase family M3 / Peptidase M3A/M3B / Neurolysin; domain 3 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor ...Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase family M3 / Peptidase M3A/M3B / Neurolysin; domain 3 / Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Neurotensin/neuromedin N / Neurolysin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMasuyer, G. / Berntsson, R.P.-A. / Teixeira, P.F. / Kmiec, B. / Glaser, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2014-5667 Sweden
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin.
Authors: Teixeira, P.F. / Masuyer, G. / Pinho, C.M. / Branca, R.M.M. / Kmiec, B. / Wallin, C. / Warmlander, S.K.T.S. / Berntsson, R.P. / Ankarcrona, M. / Graslund, A. / Lehtio, J. / Stenmark, P. / Glaser, E.
History
DepositionSep 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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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: PRO-ARG-ARG-PRO neurotensin fragment
D: PRO-ARG-ARG-PRO neurotensin fragment
P: PRO-ARG-ARG-PRO neurotensin fragment
Q: PRO-ARG-ARG-PRO neurotensin fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,28711
Polymers163,9936
Non-polymers2945
Water2,108117
1
A: Neurolysin, mitochondrial
C: PRO-ARG-ARG-PRO neurotensin fragment
P: PRO-ARG-ARG-PRO neurotensin fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1906
Polymers81,9973
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-53 kcal/mol
Surface area27720 Å2
MethodPISA
2
B: Neurolysin, mitochondrial
D: PRO-ARG-ARG-PRO neurotensin fragment
Q: PRO-ARG-ARG-PRO neurotensin fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0985
Polymers81,9973
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-49 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.329, 131.329, 195.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDPQ

#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: 78644.781 Da / Num. of mol.: 2 / Mutation: E475Q
Source method: isolated from a genetically manipulated source
Details: Catalytically impaired Human neurolysin / Source: (gene. exp.) Homo sapiens (human) / Gene: NLN, AGTBP, KIAA1226 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BYT8, neurolysin
#2: Protein/peptide
PRO-ARG-ARG-PRO neurotensin fragment


Mass: 1675.948 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Neurotensin product of the cleavage reaction by human neurolysin
Source: (synth.) Homo sapiens (human) / References: UniProt: P30990*PLUS

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Non-polymers , 4 types, 122 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 54.8 % / Description: elongated pyramidal shapes
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 46686 / % possible obs: 98.6 % / Redundancy: 5.9 % / CC1/2: 0.982 / Rmerge(I) obs: 0.01 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.632 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimless0.5.15data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I1I

1i1i


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 32.777 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 2.661 / ESU R Free: 0.368 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26786 2301 4.9 %RANDOM
Rwork0.21558 ---
obs0.21813 44361 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10826 0 10 117 10953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911049
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210556
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9714894
X-RAY DIFFRACTIONr_angle_other_deg0.869324341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46151333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68324.167528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.971152037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2091571
X-RAY DIFFRACTIONr_chiral_restr0.0580.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.794.5245359
X-RAY DIFFRACTIONr_mcbond_other0.794.5235358
X-RAY DIFFRACTIONr_mcangle_it1.4596.7756683
X-RAY DIFFRACTIONr_mcangle_other1.4596.7766684
X-RAY DIFFRACTIONr_scbond_it0.5234.6075690
X-RAY DIFFRACTIONr_scbond_other0.5234.6075690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0136.8848211
X-RAY DIFFRACTIONr_long_range_B_refined2.63234.90712284
X-RAY DIFFRACTIONr_long_range_B_other2.63134.91112281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 159 -
Rwork0.31 3274 -
obs--99.08 %
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)
10.30920.37350.18880.68670.25930.5865-0.02380.0437-0.1090.11070.0511-0.0977-0.0889-0.1066-0.02720.11430.04270.01040.065-0.03630.05152.539-17.822420.3902
21.1384-0.2015-0.61290.3760.26860.45530.08180.1271-0.01170.0211-0.06720.0515-0.0154-0.0232-0.01460.01860.01780.0010.1086-0.0690.054518.5873-48.8973-21.4954
30000000000000000.074000.07400.074000
40000000000000000.074000.07400.074000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 1101
2X-RAY DIFFRACTION2B13 - 1002

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