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- PDB-9rv5: Crystal structure of SPSB2 SPRY domain in complex with linear TAT... -

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Basic information

Entry
Database: PDB / ID: 9rv5
TitleCrystal structure of SPSB2 SPRY domain in complex with linear TAT peptide
Components
  • SPRY domain-containing SOCS box protein 2
  • Tat Peptide
KeywordsTRANSFERASE / SPSB2 / TAT Peptide / SPRY domain / SPRY domain-containing SOCS box protein 2
Function / homology
Function and homology information


SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytosol
Similarity search - Function
SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY 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 / 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
ACETATE ION / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLenz, C. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of SPSB2 SPRY domain in complex with linear TAT peptide
Authors: Lenz, C. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionJul 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPRY domain-containing SOCS box protein 2
B: Tat Peptide
C: SPRY domain-containing SOCS box protein 2
D: Tat Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8168
Polymers52,5774
Non-polymers2394
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-0 kcal/mol
Surface area17060 Å2
Unit cell
Length a, b, c (Å)40.470, 90.106, 57.817
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23849.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99619
#2: Protein/peptide Tat Peptide


Mass: 2438.758 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG3350 10% Ethylene glycol, 0.2M Sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 7, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→48.41 Å / Num. obs: 44886 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Χ2: 0.94 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.123 / Num. measured all: 15833 / Num. unique obs: 2333 / CC1/2: 0.765 / Rpim(I) all: 0.461 / Rrim(I) all: 1.216 / Χ2: 0.98 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→48.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.562 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19886 2064 5 %RANDOM
Rwork0.17133 ---
obs0.17271 39102 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.484 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å2-0 Å20.79 Å2
2---0.79 Å20 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 1.75→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 16 286 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123197
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162943
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.8194340
X-RAY DIFFRACTIONr_angle_other_deg0.4971.756752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.582528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62910474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it1.6581.8361609
X-RAY DIFFRACTIONr_mcbond_other1.6571.8351606
X-RAY DIFFRACTIONr_mcangle_it2.6773.2811997
X-RAY DIFFRACTIONr_mcangle_other2.6773.2821998
X-RAY DIFFRACTIONr_scbond_it2.3362.0791588
X-RAY DIFFRACTIONr_scbond_other2.3352.081589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7873.6912344
X-RAY DIFFRACTIONr_long_range_B_refined5.56119.783453
X-RAY DIFFRACTIONr_long_range_B_other5.56119.783454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 133 -
Rwork0.239 2823 -
obs--97.2 %

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