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- PDB-5o3y: SOD1 bound to Ebsulfur -

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Basic information

Entry
Database: PDB / ID: 5o3y
TitleSOD1 bound to Ebsulfur
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE Drug discovery ALS MND
Function / homology
Function and homology information


action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / Oxidoreductases; Acting on a sulfur group of donors / dense core granule / anterograde axonal transport / regulation of organ growth ...action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / Oxidoreductases; Acting on a sulfur group of donors / dense core granule / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / regulation of GTPase activity / myeloid cell homeostasis / superoxide anion generation / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / cellular response to cadmium ion / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / reactive oxygen species metabolic process / positive regulation of phagocytosis / thymus development / placenta development / positive regulation of cytokine production / response to amphetamine / determination of adult lifespan / regulation of mitochondrial membrane potential / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / response to nutrient levels / mitochondrial intermembrane space / negative regulation of inflammatory response / small GTPase binding / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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-sulfanyl-benzamide / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 / 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 / _citation_author.name
Revision 1.2Feb 20, 2019Group: Data collection / Derived calculations / Category: pdbx_data_processing_status / struct_conn
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)32,56710
Polymers31,6552
Non-polymers9128
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-135 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.050, 67.960, 51.180
Angle α, β, γ (deg.)90.00, 106.73, 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 / Plasmid: pET26b / 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-9JK / ~{N}-phenyl-2-sulfanyl-benzamide


Mass: 229.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOS
#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.: 313 / 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: 38.56 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75 / Details: 100 mM NaAct pH 3.75, 100 mM NaCl, 2.8 M AmSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2016
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.3→67.84 Å / Num. obs: 60537 / % possible obs: 98.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.1
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.4 / % possible all: 97.7

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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: 1.3→49.01 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.328 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18566 2943 4.9 %RANDOM
Rwork0.15144 ---
obs0.15308 57561 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.63 Å2
2--0.95 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.3→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 46 313 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192377
X-RAY DIFFRACTIONr_bond_other_d0.0020.022086
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9493239
X-RAY DIFFRACTIONr_angle_other_deg1.5412.9984836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75524.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11815349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0681510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022806
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02472
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_it1.4341.3121277
X-RAY DIFFRACTIONr_mcbond_other1.4241.3121276
X-RAY DIFFRACTIONr_mcangle_it1.9991.9871612
X-RAY DIFFRACTIONr_mcangle_other2.0011.9871613
X-RAY DIFFRACTIONr_scbond_it2.0041.5551100
X-RAY DIFFRACTIONr_scbond_other2.0021.5551097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5152.2381622
X-RAY DIFFRACTIONr_long_range_B_refined5.30518.6542593
X-RAY DIFFRACTIONr_long_range_B_other4.34517.7012525
X-RAY DIFFRACTIONr_rigid_bond_restr3.54134451
X-RAY DIFFRACTIONr_sphericity_free30.6375181
X-RAY DIFFRACTIONr_sphericity_bonded12.45854519
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 218 -
Rwork0.299 4198 -
obs--97.59 %

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