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- PDB-5ljm: Structure of SPATA2 PUB domain -

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Basic information

Entry
Database: PDB / ID: 5ljm
TitleStructure of SPATA2 PUB domain
ComponentsSpermatogenesis-associated protein 2
KeywordsCELL CYCLE / PUB domain
Function / homology
Function and homology information


protein linear deubiquitination / regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / seminiferous tubule development / ubiquitin-specific protease binding / necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling ...protein linear deubiquitination / regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / seminiferous tubule development / ubiquitin-specific protease binding / necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / fibrillar center / signaling receptor complex adaptor activity / regulation of inflammatory response / spermatogenesis / protein-containing complex binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Spermatogenesis-associated protein 2, PUB-like domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spermatogenesis-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.454 Å
AuthorsElliott, P.R. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.
Authors: Elliott, P.R. / Leske, D. / Hrdinka, M. / Bagola, K. / Fiil, B.K. / McLaughlin, S.H. / Wagstaff, J. / Volkmar, N. / Christianson, J.C. / Kessler, B.M. / Freund, S.M. / Komander, D. / Gyrd-Hansen, M.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermatogenesis-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0363
Polymers24,8511
Non-polymers1842
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-0 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.480, 51.140, 56.290
Angle α, β, γ (deg.)90.000, 105.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spermatogenesis-associated protein 2 / Spermatogenesis-associated protein PD1


Mass: 24851.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPATA2, KIAA0757, PD1 / Plasmid: pOPINK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta II / References: UniProt: Q9UM82
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6
Details: Crystals grew at 277K over two weeks in: 20 mM MES pH 6.0, 200 mM NaCl, 4 mM DTT

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→54.12 Å / Num. obs: 37750 / % possible obs: 90.2 % / Redundancy: 3 % / Biso Wilson estimate: 15.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/av σ(I): 12.1 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.45-1.482.90.3792.20.908181.2
7.97-54.123.30.038380.99199.8

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealised helices in AMPLE

Resolution: 1.454→54.117 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1877 5.01 %Random selection
Rwork0.1822 ---
obs0.1843 37458 89.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.81 Å2 / Biso mean: 27.1847 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: final / Resolution: 1.454→54.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 12 308 1959
Biso mean--21.75 38.05 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051779
X-RAY DIFFRACTIONf_angle_d0.7722413
X-RAY DIFFRACTIONf_chiral_restr0.066268
X-RAY DIFFRACTIONf_plane_restr0.005307
X-RAY DIFFRACTIONf_dihedral_angle_d21.995700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4542-1.49360.31381110.29882311242276
1.4936-1.53750.30781420.24162343248579
1.5375-1.58710.24411550.21843040319599
1.5871-1.64390.24361580.20733017317599
1.6439-1.70970.21581900.18962961315199
1.7097-1.78750.22631450.1863017316299
1.7875-1.88180.25471680.19793028319699
1.8818-1.99970.2615780.2131601167952
1.9997-2.15410.21931470.17742708285589
2.1541-2.37080.26261250.19842654277987
2.3708-2.71390.19941450.16712933307894
2.7139-3.41910.2251410.172830843225100
3.4191-54.15480.20341720.16482884305692

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