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- PDB-6key: Structural basis for the regulation of inducible nitric oxide syn... -

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Basic information

Entry
Database: PDB / ID: 6key
TitleStructural basis for the regulation of inducible nitric oxide synthase (iNOS) by the SPRY domain-containing SOCS box protein 2 (SPSB2)
Components
  • Nitric oxide synthase, inducible
  • SPRY domain-containing SOCS box protein 2
KeywordsPROTEIN BINDING/INHIBITOR / SPRY domain-containing SOCS box protein / SPSB2 / inducible nitric oxide synthase / iNOS / 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 / regulation of insulin secretion / peroxisomal matrix / ubiquitin-like ligase-substrate adaptor activity / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / 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 / circadian rhythm / peroxisome / positive regulation of interleukin-6 production / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to xenobiotic stimulus / FMN binding / Neddylation / NADP binding / regulation of cell population proliferation / flavin adenine dinucleotide binding / ubiquitin-dependent protein catabolic process / cellular response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / response to lipopolysaccharide / calmodulin binding / response to hypoxia / protein ubiquitination / intracellular signal transduction / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / 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 / 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: 1.24 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: Nitric Oxide / Year: 2021
Title: Structural basis for the regulation of inducible nitric oxide synthase by the SPRY domain-containing SOCS box protein SPSB2, an E3 ubiquitin ligase.
Authors: Li, K. / You, T. / Zhao, P. / Luo, Y. / Zhang, D. / Wei, H. / Wang, Y. / Yang, J. / Guan, X. / Kuang, Z.
History
DepositionJul 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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)23,9722
Polymers23,9722
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint1 kcal/mol
Surface area9640 Å2
Unit cell
Length a, b, c (Å)40.240, 64.080, 70.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPRY domain-containing SOCS box protein 2 / SSB-2


Mass: 22896.604 Da / Num. of mol.: 1
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: 1075.173 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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 38.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / 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: 1.24→64.08 Å / Num. obs: 52182 / % possible obs: 98.4 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Net I/σ(I): 10 / Num. measured all: 346278 / Scaling rejects: 492
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.24-1.266.60.3421763026620.9390.1410.3724.498.7
6.65-64.088.20.08630253700.9950.0310.09119.493.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 0.639 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 2553 4.9 %RANDOM
Rwork0.1843 ---
obs0.1853 49579 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 37.35 Å2 / Biso mean: 9.098 Å2 / Biso min: 3.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0 Å2
2---0.67 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 1.24→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 0 122 1724
Biso mean---15.88 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0141642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171427
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.6582227
X-RAY DIFFRACTIONr_angle_other_deg1.051.6333359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3745206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09421.18393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
LS refinement shellResolution: 1.24→1.267 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.221 166 -
Rwork0.203 3638 -
obs--98.35 %

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