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- PDB-2jk9: The structure of splA-ryanodine receptor domain and SOCS box cont... -

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Basic information

Entry
Database: PDB / ID: 2jk9
TitleThe structure of splA-ryanodine receptor domain and SOCS box containing 1 in complex with a PAR-4 peptide
Components
  • PRKC APOPTOSIS WT1 REGULATOR PROTEIN
  • SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 1
KeywordsAPOPTOSIS / TRANSCRIPTION REGULATION / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of hydrogen peroxide-mediated programmed cell death / leucine zipper domain binding / positive regulation of amyloid precursor protein biosynthetic process / SCF ubiquitin ligase complex / negative regulation of T cell receptor signaling pathway / negative regulation of B cell proliferation / actin filament bundle assembly / ubiquitin-like ligase-substrate adaptor activity / negative regulation of fibroblast proliferation / negative regulation of T cell proliferation ...positive regulation of hydrogen peroxide-mediated programmed cell death / leucine zipper domain binding / positive regulation of amyloid precursor protein biosynthetic process / SCF ubiquitin ligase complex / negative regulation of T cell receptor signaling pathway / negative regulation of B cell proliferation / actin filament bundle assembly / ubiquitin-like ligase-substrate adaptor activity / negative regulation of fibroblast proliferation / negative regulation of T cell proliferation / actin filament / apoptotic signaling pathway / positive regulation of cellular senescence / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / Neddylation / actin binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of apoptotic process / negative regulation of gene expression / intracellular membrane-bounded organelle / apoptotic process / positive regulation of gene expression / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Prostate apoptosis response 4 / : / SOCS box / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily ...Prostate apoptosis response 4 / : / SOCS box / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
SPRY domain-containing SOCS box protein 1 / PRKC apoptosis WT1 regulator protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsFilippakopoulos, P. / Bullock, A. / Keates, T. / Savitsky, P. / Murray, J.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. / Knapp, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis for Par-4 Recognition by the Spry Domain-and Socs Box-Containing Proteins Spsb1, Spsb2, and Spsb4.
Authors: Filippakopoulos, P. / Low, A. / Sharpe, T.D. / Uppenberg, J. / Yao, S. / Kuang, Z. / Savitsky, P. / Lewis, R.S. / Nicholson, S.E. / Norton, R.S. / Bullock, A.
History
DepositionAug 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 1
B: PRKC APOPTOSIS WT1 REGULATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,5082
Polymers25,5082
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-1.5 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.523, 82.957, 38.540
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 1 / SPLA-RYANODINE RECEPTOR DOMAIN AND SOCS BOX CONTAINING 1


Mass: 24059.254 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96BD6
#2: Protein/peptide PRKC APOPTOSIS WT1 REGULATOR PROTEIN / PROSTATE APOPTOSIS RESPONSE 4 PROTEIN / PAR-4 PEPTIDE


Mass: 1448.537 Da / Num. of mol.: 1 / Fragment: RESIDUES 67-81 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96IZ0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.46 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG3350, 0.2M NACL, 0.1M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 29, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→37.32 Å / Num. obs: 20678 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.64
Reflection shellResolution: 1.79→1.81 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.67 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0036refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A HOMOLOGY MODEL FROM PDB ENTRY 2FNJ

2fnj


Resolution: 1.79→83.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.774 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1063 5.1 %RANDOM
Rwork0.192 ---
obs0.194 19615 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å21.16 Å2
2---0.85 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.79→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 121 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211716
X-RAY DIFFRACTIONr_bond_other_d0.0010.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9332338
X-RAY DIFFRACTIONr_angle_other_deg0.87132760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47423.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.351513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.04831044
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.09151684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3348672
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.50311654
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.418 71
Rwork0.337 1367
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1589-0.4580.34561.0948-0.00730.97570.0588-0.1941-0.1716-0.0384-0.0385-0.04290.0979-0.0273-0.02030.0595-0.00610.01460.02980.00810.0534-2.431625.73520.8906
22.0617-0.60270.30181.5289-0.1270.9621-0.0071-0.190.3190.01380.005-0.1275-0.0802-0.07510.00210.05110.00470.02330.0276-0.03130.0681-4.603738.39822.0889
32.2349-0.31990.22431.5147-0.13570.80750.052-0.07770.0962-0.0888-0.02560.13890.0026-0.1125-0.02640.05170.00490.01760.0265-0.00580.0402-11.649934.388818.1309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 94
2X-RAY DIFFRACTION2A95 - 154
3X-RAY DIFFRACTION3A155 - 231

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