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- PDB-8ae5: Crystal structure of human legumain in complex with macrocypin 1a -

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Basic information

Entry
Database: PDB / ID: 8ae5
TitleCrystal structure of human legumain in complex with macrocypin 1a
Components
  • Legumain
  • Macrocypin-1a
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 / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cysteine-type endopeptidase inhibitor activity / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
: / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
Macrocypin-1a / Legumain
Similarity search - Component
Biological speciesHomo sapiens (human)
Macrolepiota procera (parasol mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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

Downloads & links

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Assembly

Deposited unit
A: Legumain
C: Macrocypin-1a
B: Legumain
D: Macrocypin-1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,62414
Polymers100,8354
Non-polymers1,79010
Water1,44180
1
A: Legumain
C: Macrocypin-1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0526
Polymers50,4172
Non-polymers6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Legumain
D: Macrocypin-1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5728
Polymers50,4172
Non-polymers1,1556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.178, 174.122, 112.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 26 through 288 or resid 310 through 311))
d_1ens_2(chain "C" and (resid 2 through 16 or resid 25 through 169))
d_2ens_2(chain "D" and (resid 2 through 168 or (resid 169...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYARGA1 - 263
d_12ens_1NAGNAGB
d_13ens_1NAGNAGC
d_21ens_1GLYARGE1 - 263
d_22ens_1NAGNAGF
d_23ens_1NAGNAGG
d_11ens_2GLYGLYD1 - 15
d_12ens_2GLYGLUD24 - 168
d_21ens_2GLYGLUJ1 - 160

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.874205489523, 0.0843781092326, -0.478168481573), (-0.130319380948, 0.907880113231, 0.39846023509), (0.467740976435, 0.41065074538, -0.782677675855)9.3559611053, -1.40002536093, 37.8664574402
2given(-0.92637814955, 0.0840876545834, -0.367086897591), (-0.0764827708488, 0.912431123131, 0.402019690196), (0.3687464031, 0.400498079757, -0.838824998621)9.28705369292, -0.376278768191, 36.4752315865

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 30133.838 Da / Num. of mol.: 2
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 Macrocypin-1a


Mass: 20283.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrolepiota procera (parasol mushroom)
Production host: Escherichia coli (E. coli) / References: UniProt: B9V973

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Sugars , 2 types, 5 molecules

#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: obtained synthetically
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.: 4 / 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

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Non-polymers , 2 types, 85 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Ammonium Sulfate, 500 mM LiCl

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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: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.28→47.39 Å / Num. obs: 70688 / % possible obs: 99.1 % / Redundancy: 11.361 % / Biso Wilson estimate: 74.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.114 / Χ2: 1.248 / Net I/σ(I): 13.72 / Num. measured all: 803083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.28-2.4211.4173.3940.612345011413108130.3873.55294.7
2.42-2.5911.8342.0321.1312663110701107010.692.124100
2.59-2.811.5621.0332.3311573610014100100.8881.081100
2.8-3.0610.9880.4835.03101211922592110.9660.50799.8
3.06-3.429.8480.211.1182545838483820.9920.211100
3.42-3.9512.3140.09624.4891306741574150.9980.101100
3.95-4.8311.8260.05938.4974619631063100.9990.062100
4.83-6.7911.5150.05243.6857127496149610.9990.054100
6.79-47.3910.5570.0451.0730458290428850.9990.04299.3

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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: 2.29→47.39 Å / SU ML: 0.5016 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 34.4693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 3661 5.23 %
Rwork0.2212 66370 -
obs0.223 70031 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.69 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 109 80 7054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857171
X-RAY DIFFRACTIONf_angle_d1.08199757
X-RAY DIFFRACTIONf_chiral_restr0.06821019
X-RAY DIFFRACTIONf_plane_restr0.00721259
X-RAY DIFFRACTIONf_dihedral_angle_d21.89472598
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS4.0891036832
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.836482967633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.58251010.5272190X-RAY DIFFRACTION85.55
2.32-2.350.50321350.46062554X-RAY DIFFRACTION99.59
2.35-2.390.44961560.43642491X-RAY DIFFRACTION99.4
2.39-2.420.43371420.41512551X-RAY DIFFRACTION99.52
2.42-2.460.3811510.3842540X-RAY DIFFRACTION99.78
2.46-2.50.41831440.35882526X-RAY DIFFRACTION99.44
2.5-2.540.36111300.34712527X-RAY DIFFRACTION99.36
2.54-2.590.40991330.33272554X-RAY DIFFRACTION99.67
2.59-2.640.37621490.31872555X-RAY DIFFRACTION99.82
2.64-2.690.37441290.32132543X-RAY DIFFRACTION99.85
2.69-2.750.3793240.31262382X-RAY DIFFRACTION99.63
2.75-2.8200.28062687X-RAY DIFFRACTION99.48
2.82-2.890.29823270.27042352X-RAY DIFFRACTION99.89
2.89-2.9600.25812714X-RAY DIFFRACTION99.96
2.96-3.050.306720.26132677X-RAY DIFFRACTION99.7
3.05-3.150.32543280.26162383X-RAY DIFFRACTION99.78
3.15-3.2600.26952692X-RAY DIFFRACTION99.93
3.26-3.390.28873270.25292390X-RAY DIFFRACTION99.82
3.39-3.5500.24642716X-RAY DIFFRACTION99.93
3.55-3.7400.22592710X-RAY DIFFRACTION99.96
3.74-3.970.24773270.2072400X-RAY DIFFRACTION100
3.97-4.2800.18492734X-RAY DIFFRACTION100
4.28-4.710.18323270.16922430X-RAY DIFFRACTION99.96
4.71-5.3900.16962745X-RAY DIFFRACTION100
5.39-6.780.23133270.1912449X-RAY DIFFRACTION100
6.78-47.390.402920.18592878X-RAY DIFFRACTION99.14
Refinement TLS params.Method: refined / Origin x: 3.23212958042 Å / Origin y: -53.7248821459 Å / Origin z: 3.40439353297 Å
111213212223313233
T0.729846939976 Å2-0.0292298811445 Å20.0327349610371 Å2-0.604302250591 Å2-0.00758506902525 Å2--0.805220559368 Å2
L1.03188608128 °2-0.0812368616288 °2-0.0360318489109 °2--0.177943097213 °20.147768619963 °2--0.603868019709 °2
S0.103206917667 Å °-0.068220705619 Å °0.607626553941 Å °-0.100223370497 Å °-0.122610328502 Å °0.052252955702 Å °-0.277064841128 Å °0.0305276401065 Å °0.024215390274 Å °
Refinement TLS groupSelection details: all

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