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- PDB-6jwm: Crystal structure of the SPRY domain of SPSB2 in complex with cR7... -

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Basic information

Entry
Database: PDB / ID: 6jwm
TitleCrystal structure of the SPRY domain of SPSB2 in complex with cR7, a potent cyclic peptide inhibitor of SPSB2-iNOS interaction
Components
  • Nitric oxide synthase, inducible
  • SPRY domain-containing SOCS box protein 2
KeywordsPROTEIN BINDING/INHIBITOR / SPRY domain-containing SOCS box protein / PRY-SPRY / B30.2 / inducible nitric oxide synthase / E3 ubiquitin ligase / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine binding / SCF ubiquitin ligase complex ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine binding / SCF ubiquitin ligase complex / cortical cytoskeleton / superoxide metabolic process / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / peroxisomal matrix / regulation of insulin secretion / ubiquitin-like ligase-substrate adaptor activity / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / cell redox homeostasis / innate immune response in mucosa / positive regulation of interleukin-8 production / Peroxisomal protein import / response to bacterium / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / peroxisome / circadian rhythm / cellular response to xenobiotic stimulus / Antigen processing: Ubiquitination & Proteasome degradation / FMN binding / flavin adenine dinucleotide binding / Neddylation / NADP binding / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / response to lipopolysaccharide / response to hypoxia / protein ubiquitination / calmodulin binding / intracellular signal transduction / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / B30.2/SPRY domain profile. ...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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Nitric oxide synthase, inducible / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsLi, K. / Kuang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270817 China
National Natural Science Foundation of China81571539 China
Ministry of Education (China)21617443 China
CitationJournal: To Be Published
Title: Crystal structure of SPSB2 in complex with cR7, a potent cyclic peptide inhibitor of SPSB2-iNOS interaction
Authors: Li, K. / Kuang, Z.
History
DepositionApr 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Nitric oxide synthase, inducible


Theoretical massNumber of molelcules
Total (without water)23,6992
Polymers23,6992
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint1 kcal/mol
Surface area9540 Å2
Unit cell
Length a, b, c (Å)40.060, 63.970, 68.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22896.604 Da / Num. of mol.: 1 / Fragment: UNP residues 22-220
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 Nitric oxide synthase, inducible / / Hepatocyte NOS / HEP-NOS / Inducible NO synthase / iNOS / NOS type II / Peptidyl-cysteine S-nitrosylase NOS2


Mass: 802.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35228, nitric-oxide synthase (NADPH)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.23→63.97 Å / Num. obs: 51393 / % possible obs: 99.8 % / Redundancy: 8.3 % / Net I/σ(I): 14.4
Reflection shellResolution: 1.24→1.26 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→46.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.587 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20018 2589 5 %RANDOM
Rwork0.17688 ---
obs0.17805 48738 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0 Å2
2---0.73 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.23→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 125 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171427
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.6552259
X-RAY DIFFRACTIONr_angle_other_deg1.0851.633360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64620.72996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2371516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
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_it1.1060.782839
X-RAY DIFFRACTIONr_mcbond_other1.1040.781838
X-RAY DIFFRACTIONr_mcangle_it1.6691.1751047
X-RAY DIFFRACTIONr_mcangle_other1.671.1761048
X-RAY DIFFRACTIONr_scbond_it1.9450.99825
X-RAY DIFFRACTIONr_scbond_other1.9470.991823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9261.4031212
X-RAY DIFFRACTIONr_long_range_B_refined3.659.961844
X-RAY DIFFRACTIONr_long_range_B_other3.6099.7771825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.235→1.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 185 -
Rwork0.189 3554 -
obs--99.81 %

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