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- PDB-5o40: SOD1 bound to Ebselen -

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Basic information

Entry
Database: PDB / ID: 5o40
TitleSOD1 bound to Ebselen
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide / regulation of GTPase activity / auditory receptor cell stereocilium organization / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / muscle cell cellular homeostasis / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / thymus development / superoxide dismutase activity / ovarian follicle development / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / transmission of nerve impulse / response to axon injury / reactive oxygen species metabolic process / placenta development / embryo implantation / positive regulation of superoxide anion generation / sensory perception of sound / response to amphetamine / axon cytoplasm / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / regulation of mitochondrial membrane potential / dendrite cytoplasm / locomotory behavior / positive regulation of cytokine production / glutathione metabolic process / response to hydrogen peroxide / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / negative regulation of neuron apoptotic process / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / positive regulation of MAPK cascade / intracellular iron ion homeostasis / lysosome / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCapper, M.J. / Wright, G.S.A. / Antonyuk, S.V. / Hasnain, S.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
MNDAHasnain/Apr15/833-791 United Kingdom
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: The cysteine-reactive small molecule ebselen facilitates effective SOD1 maturation.
Authors: Capper, M.J. / Wright, G.S.A. / Barbieri, L. / Luchinat, E. / Mercatelli, E. / McAlary, L. / Yerbury, J.J. / O'Neill, P.M. / Antonyuk, S.V. / Banci, L. / Hasnain, S.S.
History
DepositionMay 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
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 1.2Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,66110
Polymers31,6552
Non-polymers1,0068
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-135 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 67.840, 51.040
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15827.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 100 mM NaACT pH 4, 2.4 M AMSO4, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationMonochromator: Cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→49.01 Å / Num. obs: 39891 / % possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v0a

2v0a


Resolution: 1.5→48.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.995 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21526 2081 5.2 %RANDOM
Rwork0.16836 ---
obs0.17079 37783 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.56 Å2
2--0.63 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.5→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 46 309 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192338
X-RAY DIFFRACTIONr_bond_other_d0.0020.022059
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9623179
X-RAY DIFFRACTIONr_angle_other_deg1.223.0014784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10225.47495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.90215349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.304158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
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_it1.2751.0731251
X-RAY DIFFRACTIONr_mcbond_other1.2761.0731250
X-RAY DIFFRACTIONr_mcangle_it1.7381.6181570
X-RAY DIFFRACTIONr_mcangle_other1.7391.6181571
X-RAY DIFFRACTIONr_scbond_it1.6731.2461087
X-RAY DIFFRACTIONr_scbond_other1.6741.2471084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2071.791602
X-RAY DIFFRACTIONr_long_range_B_refined4.27915.2892561
X-RAY DIFFRACTIONr_long_range_B_other3.48614.2272468
X-RAY DIFFRACTIONr_rigid_bond_restr4.57534385
X-RAY DIFFRACTIONr_sphericity_free32.4495152
X-RAY DIFFRACTIONr_sphericity_bonded11.47254483
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 181 -
Rwork0.285 2748 -
obs--99.63 %

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