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- PDB-6dn8: SPRY domain-containing SOCS box protein 2 complexed with (GZJ)VDI... -

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Basic information

Entry
Database: PDB / ID: 6dn8
TitleSPRY domain-containing SOCS box protein 2 complexed with (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
Components
  • (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
  • SPRY domain-containing SOCS box protein 4
KeywordsIMMUNE SYSTEM/INHIBITOR / proteasomal degradation / nitric oxide / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex
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 / protein ubiquitination ...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 / protein ubiquitination / intracellular signal transduction / 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. / SPRY domain / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
(GZJ)VDINNN(CY3) Cyclic peptide inhibitor / ACETATE ION / SPRY domain-containing SOCS box protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsLaw, R.H.P. / Caradoc-Davies, T.T. / Norton, R.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1099428 Australia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent.
Authors: Sadek, M.M. / Barlow, N. / Leung, E.W.W. / Williams-Noonan, B.J. / Yap, B.K. / Shariff, F.M. / Caradoc-Davies, T.T. / Nicholson, S.E. / Chalmers, D.K. / Thompson, P.E. / Law, R.H.P. / Norton, R.S.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site_gen.label_asym_id / _struct_site_gen.label_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 4
B: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
C: SPRY domain-containing SOCS box protein 4
D: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
E: SPRY domain-containing SOCS box protein 4
F: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,90212
Polymers78,4366
Non-polymers4656
Water9,350519
1
A: SPRY domain-containing SOCS box protein 4
B: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3014
Polymers26,1452
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SPRY domain-containing SOCS box protein 4
D: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3975
Polymers26,1452
Non-polymers2513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: SPRY domain-containing SOCS box protein 4
F: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2043
Polymers26,1452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.020, 109.370, 118.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-303-

SO4

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Components

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


Mass: 25228.396 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB4, SSB4 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q96A44
#2: Protein/peptide (GZJ)VDINNN(CY3) Cyclic peptide inhibitor


Type: Cyclic peptide / Class: Inhibitor / Mass: 916.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: (GZJ)VDINNN(CY3) Cyclic peptide inhibitor
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2M NH4SO4, 0.1M NaAc, 25% PEG4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→45.27 Å / Num. obs: 64838 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 24.51 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.03 / Net I/av σ(I): 16.2 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.7 / Rpim(I) all: 0.295

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.75→45.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3178 4.91 %RANDOM
Rwork0.193 ---
obs0.194 64787 99.8 %-
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.3926 Å20 Å20 Å2
2---6.06 Å20 Å2
3---0.6674 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.75→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 66 519 5280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014888HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046638HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1599SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes731HARMONIC5
X-RAY DIFFRACTIONt_it4888HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion15.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion583SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6042SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2892 222 4.73 %
Rwork0.2525 4468 -
all0.2542 4690 -
obs--99.91 %
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)
10.29670.3910.08150.290.33980.8212-0.00960.0483-0.0140.09840.02270.0076-0.00370.0722-0.0131-0.16390.0096-0.0089-0.1341-0.0213-0.145614.2229129.177129.798
20.2021-0.1162-0.1140.2420.41070.3631-0.00810.0104-0.09520.1460.00260.00820.0440.0230.0055-0.0885-0.0071-0.0033-0.2034-0.0235-0.1457-6.8501104.175140.303
30.0217-0.127-0.33330.20790.29491.25450.0256-0.0065-0.0315-0.0898-0.0173-0.02660.0878-0.1064-0.0083-0.1286-0.0264-0.0063-0.1267-0.0221-0.1545-18.5859128.14162.58
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ E|* }

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