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- PDB-32tc: Crystal structure of the human SPRY domain-containing SOCS box pr... -

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Basic information

Entry
Database: PDB / ID: 32tc
TitleCrystal structure of the human SPRY domain-containing SOCS box protein SPSB4 bound to fragment Z104474228
ComponentsSPRY domain-containing SOCS box protein 4
KeywordsPROTEIN BINDING / E3 ligase / SOCS Box / fragment
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction ...positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / 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
: / 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 ...: / 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
3-methylthiophene-2-carboxylic acid / CITRATE ANION / SPRY domain-containing SOCS box protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsRandall, G.T. / Costello, N.A. / Koekemoer, L. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Crystallographic fragment screening of a human E3 ligase
Authors: Randall, G.T. / Costello, N.A. / Koekemoer, L. / von Delft, F.
History
DepositionJul 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6008
Polymers22,7571
Non-polymers8437
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-30 kcal/mol
Surface area9430 Å2
Unit cell
Length a, b, c (Å)63.617, 84.000, 68.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

CL

21A-524-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SPRY domain-containing SOCS box protein 4 / SSB-4


Mass: 22756.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal Ser-Met from affinity tag, residues 28-233
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB4, SSB4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96A44

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-60P / 3-methylthiophene-2-carboxylic acid


Mass: 142.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Sodium Citrate pH 5.5, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9156 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 26, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9156 Å / Relative weight: 1
ReflectionResolution: 1.56→31.81 Å / Num. obs: 26521 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.081 / Net I/σ(I): 4.6
Reflection shellResolution: 1.56→1.59 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1285 / CC1/2: 0.458 / Rpim(I) all: 0.88 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→31.81 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 1339 5.09 %
Rwork0.2024 24963 -
obs0.2047 26302 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 1.56→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 51 140 1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711690
X-RAY DIFFRACTIONf_angle_d0.99852308
X-RAY DIFFRACTIONf_chiral_restr0.0602236
X-RAY DIFFRACTIONf_plane_restr0.0104309
X-RAY DIFFRACTIONf_dihedral_angle_d8.1778248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.610.36831350.36262330X-RAY DIFFRACTION95.28
1.61-1.680.42711330.34632459X-RAY DIFFRACTION98.56
1.68-1.760.36491250.30692494X-RAY DIFFRACTION99.39
1.76-1.850.32561250.26152474X-RAY DIFFRACTION99.81
1.85-1.960.28871200.23912511X-RAY DIFFRACTION99.62
1.96-2.120.23581130.19772519X-RAY DIFFRACTION99.81
2.12-2.330.24981370.20942512X-RAY DIFFRACTION99.85
2.33-2.670.25481440.18752505X-RAY DIFFRACTION99.96
2.67-3.360.22971420.16682539X-RAY DIFFRACTION99.89
3.36-31.810.18681650.15422620X-RAY DIFFRACTION99.75

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