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

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Basic information

Entry
Database: PDB / ID: 32rm
TitleCrystal structure of the human SPRY domain-containing SOCS box protein SPSB4 - Apo
ComponentsSPRY domain-containing SOCS box protein 4
KeywordsPROTEIN BINDING / E3 ligase / SOCS Box / apo
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
CITRATE ANION / SPRY domain-containing SOCS box protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRandall, G.T. / Kot, E. / 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. / Kot, E. / Koekemoer, L. / von Delft, F.
History
DepositionJul 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9813
Polymers22,7571
Non-polymers2252
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-5 kcal/mol
Surface area9680 Å2
Unit cell
Length a, b, c (Å)63.740, 83.802, 68.232
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-302-

CL

21A-469-

HOH

31A-531-

HOH

41A-554-

HOH

51A-555-

HOH

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Components

#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
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.96 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 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→41.9 Å / Num. obs: 26844 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 17.12 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.095 / Net I/σ(I): 7.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1300 / CC1/2: 0.342 / Rpim(I) all: 1.272 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.9 Å / SU ML: 0.1963 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 1349 5.03 %
Rwork0.1865 25460 -
obs0.1878 26809 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.47 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 0 14 155 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631668
X-RAY DIFFRACTIONf_angle_d0.96092275
X-RAY DIFFRACTIONf_chiral_restr0.0605238
X-RAY DIFFRACTIONf_plane_restr0.0103302
X-RAY DIFFRACTIONf_dihedral_angle_d7.6258236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.31631390.29372493X-RAY DIFFRACTION99.4
1.61-1.670.27551230.27052500X-RAY DIFFRACTION99.92
1.67-1.750.28451540.24862504X-RAY DIFFRACTION99.85
1.75-1.840.28131470.21812505X-RAY DIFFRACTION99.92
1.84-1.950.22761320.19352544X-RAY DIFFRACTION99.93
1.95-2.10.22061230.18692532X-RAY DIFFRACTION100
2.1-2.320.19831390.16932536X-RAY DIFFRACTION99.89
2.32-2.650.19741030.17832594X-RAY DIFFRACTION100
2.65-3.340.18961370.16912575X-RAY DIFFRACTION100
3.34-41.90.18631520.16892677X-RAY DIFFRACTION99.96
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)
11.61287662187-0.948909274162-0.4225463838913.40592387454-4.046545898798.86857675592-0.00695617407198-0.106321665395-0.101517296958-0.0479510960843-0.195118633415-0.2672125582010.1971588887710.04661130927960.201704560560.153828207736-0.0093209384663-0.009163536202180.1699912519810.001428072013250.21129689809923.34705449654.56422596652-8.85972087614
22.27395039974-0.986431900298-2.633330715161.760226626482.049871335594.626536262280.07614687683570.03945795059450.12641080469-0.235556366207-0.002484363811860.0490354260832-0.303942045815-0.0923695259241-0.06731926942770.1354174401890.0111158086493-0.01359262532560.1208533984340.02722885140810.1481305467257.8300814082426.5211524619-10.5846088354
31.56591289416-0.468462974623-0.5367752398051.292034375710.6647499212412.575398525150.00541106959471-0.06486615803150.01907561315880.0544380425404-0.01361210355190.0417709411145-0.0680050899305-0.07523552446650.009938673206720.0967693115536-0.00135285647229-0.01407638475690.09737101496130.006522349451690.1203178556545.6691485289518.9553236398-0.748936065826
42.139153116750.498852663380.3627456450292.700494723450.5239690209323.361202834320.0136524249548-0.129560720462-0.08737632982180.188174508723-0.0170742990561-0.003835806986170.195276629938-0.0183525120197-0.004466359330390.1129999225130.0107709491879-0.00630267549760.103397519429-0.002636970507990.12722149588512.88388906899.422580323932.39363231005
52.07533588724-0.0941316819409-0.1650466793394.05238424825-1.315506185381.399100185960.118719861763-0.215540983288-0.360347759883-0.2094372839880.04654809300420.02727141690570.0866899451474-0.0148269053868-0.1858750968660.1544413870140.006251342347280.02520409432570.141127926076-0.02872071318650.10866354805912.2685196466.03190252169-5.29599146563
62.1908320788-1.07744006592-1.474239626831.589420407141.483825537724.03800499112-0.004896380897790.01403442338110.0131215538276-0.1340318566650.03847856046790.0073589147389-0.0424009445130.134313645856-0.04423861236380.109285394972-0.00843718486082-0.01270850314270.08119211582870.0195630835910.10300381237610.809534450620.3508205702-6.87709600557
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 42 )26 - 421 - 17
22chain 'A' and (resid 43 through 77 )43 - 7718 - 52
33chain 'A' and (resid 78 through 138 )78 - 13853 - 113
44chain 'A' and (resid 139 through 191 )139 - 191114 - 166
55chain 'A' and (resid 192 through 209 )192 - 209167 - 184
66chain 'A' and (resid 210 through 232 )210 - 232185 - 207

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