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- PDB-3f2o: Crystal Structure of human splA/ryanodine receptor domain and SOC... -

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Basic information

Entry
Database: PDB / ID: 3f2o
TitleCrystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide
Components
  • 20-mer peptide from ATP-dependent RNA helicase vasa
  • SPRY domain-containing SOCS box protein 1
KeywordsAPOPTOSIS/HYDROLASE / apoptosis / nucleus / transcription regulation / SGC / Structural Genomics Consortium / Phosphoprotein / Ubl conjugation pathway / ATP-binding / Developmental protein / Differentiation / Helicase / Hydrolase / Nucleotide-binding / Oogenesis / APOPTOSIS-HYDROLASE COMPLEX
Function / homology
Function and homology information


secondary piRNA processing / posterior cell cortex / gamete generation / P granule / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / ubiquitin-like ligase-substrate adaptor activity / protein localization ...secondary piRNA processing / posterior cell cortex / 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 / protein ubiquitination / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / SOCS box / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain ...Ded1/Dbp1, DEAD-box helicase domain / SOCS box / SOCS box domain / SOCS box domain profile. / SOCS_box / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFilippakopoulos, P. / Sharpe, T. / Keates, T. / Murray, J.W. / Savitsky, P. / Roos, A. / 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. / 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
DepositionOct 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: SPRY domain-containing SOCS box protein 1
C: 20-mer peptide from ATP-dependent RNA helicase vasa
D: 20-mer peptide from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)58,0574
Polymers58,0574
Non-polymers00
Water5,170287
1
A: SPRY domain-containing SOCS box protein 1
C: 20-mer peptide from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)29,0292
Polymers29,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-3 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: SPRY domain-containing SOCS box protein 1
D: 20-mer peptide from ATP-dependent RNA helicase vasa


Theoretical massNumber of molelcules
Total (without water)29,0292
Polymers29,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-3 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.665, 80.654, 86.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
/ NCS ensembles :
ID
1
2

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Components

#1: Protein SPRY domain-containing SOCS box protein 1 / SSB-1


Mass: 26530.922 Da / Num. of mol.: 2 / Fragment: residues 1-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB1, SSB1 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q96BD6
#2: Protein/peptide 20-mer peptide from ATP-dependent RNA helicase vasa


Mass: 2497.696 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Drosophila melanogaster (Fruit fly)
References: UniProt: P09052, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.2M NaCl, 0.1M BisTris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: MAR225 / Detector: CCD / Date: Apr 10, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.05→38.24 Å / Num. obs: 34014 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2 / Num. unique all: 4899 / Rsym value: 0.649 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0036refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JK9

2jk9


Resolution: 2.05→38.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.495 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23198 1722 5.1 %RANDOM
Rwork0.17954 ---
all0.18215 32301 --
obs0.18215 32246 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 0 287 3774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213582
X-RAY DIFFRACTIONr_bond_other_d0.0020.022372
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9324879
X-RAY DIFFRACTIONr_angle_other_deg0.87735746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41423.523176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5361526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it3.39932185
X-RAY DIFFRACTIONr_mcbond_other1.5033888
X-RAY DIFFRACTIONr_mcangle_it4.54153520
X-RAY DIFFRACTIONr_scbond_it7.00181397
X-RAY DIFFRACTIONr_scangle_it8.586111359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1189medium positional0.210.5
11A1512loose positional0.380.05
22C190loose positional0.070.05
11A1189medium thermal1.432
11A1512loose thermal1.4610
22D190loose thermal4.1110
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 108 -
Rwork0.238 2374 -
obs--99.96 %
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)
10.9989-0.3122-0.31281.41570.21261.20230.02640.01490.0193-0.1747-0.0384-0.0850.004-0.01190.0120.141-0.00130.0340.1012-0.02520.2032-1.4167.37623.345
21.28230.1067-0.47151.46020.58371.36610.00060.05130.0223-0.23910.0514-0.2178-0.05550.0798-0.05190.1549-0.00520.04870.1072-0.01470.225.5444.45718.212
33.14160.527-0.61340.61240.03450.2476-0.0116-0.22630.17250.01610.0160.0253-0.01680.0496-0.00440.11640-0.00470.2195-0.03390.1509-3.03422.28155.123
41.44490.1532-0.64530.89360.37470.9332-0.0944-0.283-0.08630.1577-0.00560.03580.16680.11130.10.15510.00930.030.22650.03140.1609-5.10212.11956.424
56.2669-4.2502-1.81763.6354-0.18263.2086-0.4875-0.0647-0.36390.16870.1820.13240.5346-0.17450.30550.3104-0.02440.0420.1896-0.00080.2199-5.224-2.06342.622
62.2780.212-1.36118.1553-0.26878.9286-0.28390.3718-0.888-0.2849-0.4183-0.03420.8085-0.8160.70220.1129-0.12020.12650.3211-0.12370.3693-16.432-3.52332.943
78.8898-0.10082.12650.2176-0.03960.5161-0.2388-0.3433-0.2421-0.190.1648-0.016-0.0649-0.06350.0740.186-0.0430.02960.2880.03790.285118.88222.98951.097
818.1227.5442-8.47747.9043-5.77615.04050.3591-1.34150.62260.5132-0.3663-0.1939-0.29070.54040.00720.2126-0.03940.0410.3297-0.12050.2815.0731.1860.915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 148
2X-RAY DIFFRACTION2A149 - 233
3X-RAY DIFFRACTION3B30 - 139
4X-RAY DIFFRACTION4B140 - 233
5X-RAY DIFFRACTION5C184 - 193
6X-RAY DIFFRACTION6C194 - 201
7X-RAY DIFFRACTION7D184 - 192
8X-RAY DIFFRACTION8D193 - 198

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