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- PDB-4nom: Crystal structure of asparaginyl endopeptidase (AEP)/Legumain act... -

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Basic information

Entry
Database: PDB / ID: 4nom
TitleCrystal structure of asparaginyl endopeptidase (AEP)/Legumain activated at pH 4.5
ComponentsLegumainAsparagine endopeptidase
KeywordsHYDROLASE / new fold / asparaginyl endopeptidase / substrate / extracellular
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / MHC class II antigen presentation / positive regulation of endothelial cell chemotaxis / response to acidic pH ...Trafficking and processing of endosomal TLR / negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / MHC class II antigen presentation / positive regulation of endothelial cell chemotaxis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / proteolysis involved in protein catabolic process / positive regulation of mitotic cell cycle / lysosomal lumen / positive regulation of long-term synaptic potentiation / 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 region / cytoplasm
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold ...Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.006 Å
AuthorsZhao, L. / Hua, T. / Ru, H. / Ni, X. / Shaw, N. / Jiao, L. / Ding, W. / Qu, L. / Ouyang, S. / Liu, Z.J.
CitationJournal: Cell Res. / Year: 2014
Title: Structural analysis of asparaginyl endopeptidase reveals the activation mechanism and a reversible intermediate maturation stage.
Authors: Zhao, L. / Hua, T. / Crowley, C. / Ru, H. / Ni, X. / Shaw, N. / Jiao, L. / Ding, W. / Qu, L. / Hung, L.W. / Huang, W. / Liu, L. / Ye, K. / Ouyang, S. / Cheng, G. / Liu, Z.J.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legumain


Theoretical massNumber of molelcules
Total (without water)50,2671
Polymers50,2671
Non-polymers00
Water2,846158
1
A: Legumain

A: Legumain


Theoretical massNumber of molelcules
Total (without water)100,5342
Polymers100,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area1630 Å2
ΔGint-10 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.952, 167.721, 51.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-607-

HOH

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Components

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


Mass: 50266.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgmn, Prsc1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89017, legumain
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris-HCl, pH 8.5, and 20% PEG 2,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 32142 / Num. obs: 32142 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.006→32.623 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1615 5.02 %RANDOM
Rwork0.2044 ---
all0.2428 32142 --
obs0.2063 32142 92.35 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.454 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.0744 Å2-0 Å20 Å2
2---13.6003 Å2-0 Å2
3---27.6747 Å2
Refinement stepCycle: LAST / Resolution: 2.006→32.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 158 3424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073351
X-RAY DIFFRACTIONf_angle_d1.0424545
X-RAY DIFFRACTIONf_dihedral_angle_d16.5931227
X-RAY DIFFRACTIONf_chiral_restr0.072492
X-RAY DIFFRACTIONf_plane_restr0.005587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0057-2.06470.3282760.25951639X-RAY DIFFRACTION60
2.0647-2.13130.2933970.2411980X-RAY DIFFRACTION74
2.1313-2.20750.3061170.22942300X-RAY DIFFRACTION85
2.2075-2.29580.33531340.24122505X-RAY DIFFRACTION92
2.2958-2.40030.28141670.22552641X-RAY DIFFRACTION98
2.4003-2.52680.28951430.23072725X-RAY DIFFRACTION100
2.5268-2.68510.31971400.23262736X-RAY DIFFRACTION100
2.6851-2.89220.27271510.22712753X-RAY DIFFRACTION100
2.8922-3.18310.2871540.22032722X-RAY DIFFRACTION100
3.1831-3.64320.22811510.20532764X-RAY DIFFRACTION100
3.6432-4.5880.18031550.1622797X-RAY DIFFRACTION100
4.588-32.62740.20081300.19252965X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 42.4124 Å / Origin y: 22.4794 Å / Origin z: 28.143 Å
111213212223313233
T0.235 Å20.0294 Å2-0.0012 Å2-0.2344 Å2-0.0678 Å2--0.2117 Å2
L1.0536 °2-0.2675 °20.0453 °2-1.3775 °2-0.5076 °2--0.7344 °2
S0.0909 Å °0.1207 Å °0.0166 Å °-0.0778 Å °-0.1089 Å °0.0027 Å °0.0882 Å °0.0672 Å °0.0174 Å °
Refinement TLS groupSelection details: all

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