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- PDB-9i15: Crystal structure of SET cleaved after Asn175 by legumain -

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Basic information

Entry
Database: PDB / ID: 9i15
TitleCrystal structure of SET cleaved after Asn175 by legumain
ComponentsIsoform 2 of Protein SET
KeywordsDNA BINDING PROTEIN / I2PP2A / TAF-1
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / negative regulation of neuron apoptotic process / DNA replication ...HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / negative regulation of neuron apoptotic process / DNA replication / negative regulation of DNA-templated transcription / chromatin binding / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsHorak, C. / Brandstetter, H. / Dall, E.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundY1469 Austria
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Conformational and Functional Regulation of SET by Legumain Cleavage.
Authors: Horak, C. / Wieland, A.C. / Klaushofer, R. / Briza, P. / Brandstetter, H. / Dall, E.
History
DepositionJan 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Isoform 2 of Protein SET
A: Isoform 2 of Protein SET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3304
Polymers49,2502
Non-polymers802
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.540, 78.170, 55.120
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoform 2 of Protein SET / HLA-DR-associated protein II / Inhibitor of granzyme A-activated DNase / IGAAD / PHAPII / ...HLA-DR-associated protein II / Inhibitor of granzyme A-activated DNase / IGAAD / PHAPII / Phosphatase 2A inhibitor I2PP2A / I-2PP2A / Template-activating factor I / TAF-I


Mass: 24624.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SET / Production host: Escherichia coli (E. coli) / References: UniProt: Q01105
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 26 % PEG 400, 0.2 M calcium chloride dihydrate and 0.1 M Hepes pH 6.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 16297 / % possible obs: 98.8 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 8.7
Reflection shellResolution: 2.47→2.53 Å / Rmerge(I) obs: 1.789 / Num. unique obs: 1149 / CC1/2: 0.202 / Rrim(I) all: 1.925

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→45.03 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 813 5.01 %
Rwork0.2228 --
obs0.2255 16243 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.47→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 2 27 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033153
X-RAY DIFFRACTIONf_angle_d0.6384261
X-RAY DIFFRACTIONf_dihedral_angle_d21.5861180
X-RAY DIFFRACTIONf_chiral_restr0.043443
X-RAY DIFFRACTIONf_plane_restr0.005559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.620.45461360.36542590X-RAY DIFFRACTION100
2.62-2.830.33481350.31862548X-RAY DIFFRACTION99
2.83-3.110.37121340.28972547X-RAY DIFFRACTION99
3.11-3.560.28991320.23822504X-RAY DIFFRACTION96
3.56-4.480.2581360.18622597X-RAY DIFFRACTION100
4.49-45.030.2271400.18682644X-RAY DIFFRACTION100

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