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- PDB-4emo: Crystal structure of the PH domain of SHARPIN -

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Basic information

Entry
Database: PDB / ID: 4emo
TitleCrystal structure of the PH domain of SHARPIN
ComponentsSharpinLloyd Sharpin
KeywordsPROTEIN BINDING / Pleckstrin homology (PH) domain / LUBAC / SIPL1 / linear ubiquitin / HOIL-1L / HOIP
Function / homology
Function and homology information


apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization ...apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / negative regulation of inflammatory response / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / synapse / dendrite / protein-containing complex binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Sharpin, PH domain / Sharpin PH domain / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...Sharpin, PH domain / Sharpin PH domain / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsStieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Analysis of SHARPIN, a Subunit of a Large Multi-protein E3 Ubiquitin Ligase, Reveals a Novel Dimerization Function for the Pleckstrin Homology Superfold.
Authors: Stieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sharpin
B: Sharpin
C: Sharpin
D: Sharpin


Theoretical massNumber of molelcules
Total (without water)53,4224
Polymers53,4224
Non-polymers00
Water1,54986
1
A: Sharpin
D: Sharpin


Theoretical massNumber of molelcules
Total (without water)26,7112
Polymers26,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area10700 Å2
MethodPISA
2
B: Sharpin
C: Sharpin


Theoretical massNumber of molelcules
Total (without water)26,7112
Polymers26,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-11 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.550, 61.550, 222.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Sharpin / Lloyd Sharpin / Shank-associated RH domain-interacting protein / Shank-interacting protein-like 1 / hSIPL1


Mass: 13355.524 Da / Num. of mol.: 4 / Mutation: L21M, L101M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSEC0216, SHARPIN, SIPL1 / Plasmid: pGex4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0F6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.98 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 4M sodium formate, pH 7.4, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9799 Å
DetectorType: ADSC / Detector: CCD / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 17.17 / Number: 213897 / Rmerge(I) obs: 0.071 / Χ2: 0.95 / D res high: 2 Å / D res low: 30 Å / Num. obs: 55100 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
43096.610.0420.943.9
3.1749910.0661.0163.9
2.773.1799.510.0651.0173.9
2.522.7799.710.0980.9353.9
2.342.5299.810.1540.9093.9
2.22.3499.910.220.9473.9
2.092.299.910.3120.8883.9
22.0998.310.4830.9413.8
ReflectionResolution: 2→30 Å / Num. obs: 29888 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.071 / Χ2: 0.949 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.093.80.48367900.941198.3
2.09-2.23.90.31269770.888199.9
2.2-2.343.90.2269340.947199.9
2.34-2.523.90.15469150.909199.8
2.52-2.773.90.09869120.935199.7
2.77-3.173.90.06569141.017199.5
3.17-43.90.06668991.016199
4-303.90.04267590.94196.6

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.73 / FOM acentric: 0.76 / FOM centric: 0.62 / Reflection: 17560 / Reflection acentric: 14320 / Reflection centric: 3240
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.9-29.7220.90.940.84863490373
4.3-6.90.890.930.7724581815643
3.4-4.30.870.90.7529602382578
3-3.40.790.820.6229682461507
2.6-30.650.680.4351354407728
2.4-2.60.530.550.3531762765411

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2697 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8012 / SU B: 4.362 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1973 / SU Rfree: 0.1864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1520 5.1 %RANDOM
Rwork0.2092 ---
obs0.2122 29888 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.58 Å2 / Biso mean: 34.5554 Å2 / Biso min: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 0 86 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193264
X-RAY DIFFRACTIONr_angle_refined_deg2.1351.9924452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28522.353136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1061536
X-RAY DIFFRACTIONr_chiral_restr0.1520.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222548
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 87 -
Rwork0.24 1794 -
all-1881 -
obs--96.26 %

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