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- PDB-3emw: Crystal Structure of human splA/ryanodine receptor domain and SOC... -

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Basic information

Entry
Database: PDB / ID: 3emw
TitleCrystal Structure of human splA/ryanodine receptor domain and SOCS box containing 2 (SPSB2) in complex with a 20-residue VASA peptide
Components
  • Peptide (VASA)
  • SPRY domain-containing SOCS box protein 2
KeywordsAPOPTOSIS / Apoptosis nucleus / UBL conjugation pathwayc / CL transcription regulation / Transcription / Phosphoprotein / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


posterior cell cortex / secondary piRNA processing / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization ...posterior cell cortex / secondary piRNA processing / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA helicase activity / cell differentiation / intracellular signal transduction / RNA helicase / protein ubiquitination / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. ...Ded1/Dbp1, DEAD-box helicase domain / SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase vasa / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Filippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A.K. / Pike, A.C.W. / Von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
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.N.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 2
B: Peptide (VASA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5966
Polymers26,3472
Non-polymers2484
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint6.5 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.470, 61.963, 118.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPRY domain-containing SOCS box protein 2 / SPSB2 / SSB-2 / Gene-rich cluster protein C9


Mass: 23849.627 Da / Num. of mol.: 1 / Fragment: UNP residues 26-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q99619
#2: Protein/peptide Peptide (VASA)


Mass: 2497.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P09052*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.178M Na/KPO4, 17.8% PEG3350, 8.88% EtGly, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975653 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975653 Å / Relative weight: 1
ReflectionResolution: 1.8→42.83 Å / Num. obs: 24366 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.22 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3494 / Rsym value: 0.618 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK9

2jk9


Resolution: 1.8→42.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.491 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21593 1239 5.1 %RANDOM
Rwork0.17796 ---
all0.17995 23115 --
obs0.17995 23073 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.523 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2--0.97 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 16 138 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211636
X-RAY DIFFRACTIONr_bond_other_d0.0020.021130
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9632217
X-RAY DIFFRACTIONr_angle_other_deg0.95332732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3223.37874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81615245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.461513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_mcbond_it3.34831022
X-RAY DIFFRACTIONr_mcbond_other1.1743426
X-RAY DIFFRACTIONr_mcangle_it4.47951621
X-RAY DIFFRACTIONr_scbond_it6.898614
X-RAY DIFFRACTIONr_scangle_it8.46511596
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 87 -
Rwork0.233 1665 -
obs--99.94 %
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)
13.301-2.3859-3.970811.4412-0.07516.9983-0.1075-0.13820.25970.2783-0.0075-0.6335-0.09471.01430.1150.1238-0.0202-0.01780.1489-0.070.21224.31337.260731.4895
21.82770.52970.292.24870.36781.83070.0645-0.08570.0606-0.12830.04720.0815-0.1639-0.1821-0.1117-0.0175-0.003-0.00070.00180.03410.00849.266524.329842.0027
32.1064-0.0929-0.14421.8770.17151.96110.0445-0.1437-0.29060.04370.0779-0.04040.1755-0.0389-0.1224-0.0117-0.028-0.0419-0.01760.03670.031814.74513.783843.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 32
2X-RAY DIFFRACTION2A33 - 121
3X-RAY DIFFRACTION3A122 - 219

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