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- PDB-8ae4: Crystal structure of human legumain in complex with Clitocypin 2 -

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Basic information

Entry
Database: PDB / ID: 8ae4
TitleCrystal structure of human legumain in complex with Clitocypin 2
Components
  • Clitocypin-2
  • Legumain
KeywordsHYDROLASE / cysteine protease / ligase / asparaginyl endopeptidase / AEP / inhibitor / exosite / active site / substrate
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / endolysosome lumen / response to acidic pH / positive regulation of monocyte chemotaxis ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / endolysosome lumen / response to acidic pH / positive regulation of monocyte chemotaxis / dendritic spine organization / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / cysteine-type endopeptidase inhibitor activity / endopeptidase activator activity / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / cellular response to calcium ion / proteolysis involved in protein catabolic process / protein maturation / positive regulation of long-term synaptic potentiation / antigen processing and presentation of exogenous peptide antigen via MHC class II / tau protein binding / memory / cellular response to amyloid-beta / apical part of cell / late endosome / peptidase activity / negative regulation of neuron apoptotic process / lysosome / negative regulation of gene expression / cysteine-type endopeptidase activity / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Proteinase inhibitor I48, clitocypin / Peptidase inhibitor clitocypin / Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
Clitocypin-2 / Legumain
Similarity search - Component
Biological speciesHomo sapiens (human)
Clitocybe nebularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsElamin, T. / Brandstetter, H. / Dall, E.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP31867 Austria
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural and functional studies of legumain-mycocypin complexes revealed a competitive, exosite-regulated mode of interaction.
Authors: Elamin, T. / Santos, N.P. / Briza, P. / Brandstetter, H. / Dall, E.
History
DepositionJul 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legumain
B: Clitocypin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0545
Polymers48,1872
Non-polymers8673
Water5,819323
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, enzyme-inhibitor complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint9 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.467, 63.628, 85.532
Angle α, β, γ (deg.)90.000, 102.057, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Legumain / Asparaginyl endopeptidase / Protease / cysteine 1


Mass: 30147.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q99538, legumain
#2: Protein Clitocypin-2 / Cysteine protease inhibitor clt2


Mass: 18039.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitocybe nebularis (fungus) / Gene: clt2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3Y9I4
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 4.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.79→41.82 Å / Num. obs: 40893 / % possible obs: 97 % / Redundancy: 7.74 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 11.21
Reflection shellResolution: 1.79→1.9 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5729 / CC1/2: 0.49 / Rrim(I) all: 1.46

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7o50

7o50


Resolution: 1.79→41.53 Å / SU ML: 0.2326 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.8157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 2001 4.9 %
Rwork0.1915 38875 -
obs0.1923 40876 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.94 Å2
Refinement stepCycle: LAST / Resolution: 1.79→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 56 323 3689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753465
X-RAY DIFFRACTIONf_angle_d1.02394715
X-RAY DIFFRACTIONf_chiral_restr0.0787504
X-RAY DIFFRACTIONf_plane_restr0.0101616
X-RAY DIFFRACTIONf_dihedral_angle_d23.6101489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.39671120.32122204X-RAY DIFFRACTION77.02
1.83-1.880.34571320.29092495X-RAY DIFFRACTION88.6
1.88-1.940.3221450.25982850X-RAY DIFFRACTION99.11
1.94-20.24821400.232827X-RAY DIFFRACTION99.93
2-2.070.24881490.22362856X-RAY DIFFRACTION99.87
2.07-2.160.23031400.21352840X-RAY DIFFRACTION99.87
2.16-2.250.23041500.19612871X-RAY DIFFRACTION99.9
2.26-2.370.19231500.19592860X-RAY DIFFRACTION99.9
2.37-2.520.22691480.20222840X-RAY DIFFRACTION99.9
2.52-2.720.21391450.19542863X-RAY DIFFRACTION99.87
2.72-2.990.23741520.192821X-RAY DIFFRACTION98.94
2.99-3.420.19711410.17692742X-RAY DIFFRACTION95.5
3.42-4.310.1431480.15352885X-RAY DIFFRACTION99.34
4.31-41.530.18141490.17382921X-RAY DIFFRACTION99.45

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