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- PDB-7t8f: G93A mutant of human SOD1 bound with Ebselen in P21 space group -

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Basic information

Entry
Database: PDB / ID: 7t8f
TitleG93A mutant of human SOD1 bound with Ebselen in P21 space group
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / ALS / Drug discovery
Function / homology
Function and homology information


action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to carbon monoxide / response to antipsychotic drug / neurofilament cytoskeleton organization / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / 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 / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / 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 / dendrite cytoplasm / embryo implantation / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / positive regulation of phagocytosis / thymus development / response to amphetamine / placenta development / positive regulation of cytokine production / determination of adult lifespan / regulation of mitochondrial membrane potential / response to nutrient levels / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / 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 / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / ACETATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAmporndanai, K. / Hasnain, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateWA1128 United States
CitationJournal: Sci Rep / Year: 2024
Title: Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement.
Authors: Watanabe, S. / Amporndanai, K. / Awais, R. / Latham, C. / Awais, M. / O'Neill, P.M. / Yamanaka, K. / Hasnain, S.S.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jun 5, 2024Group: 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)32,5569
Polymers31,6832
Non-polymers8737
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-89 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.672, 67.989, 50.422
Angle α, β, γ (deg.)90.000, 105.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 2 - 152 / Label seq-ID: 2 - 152

Dom-IDAuth asym-IDLabel asym-ID
1AA
2FB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 15841.586 Da / Num. of mol.: 2 / Mutation: G93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 22, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→67.99 Å / Num. obs: 49165 / % possible obs: 99.4 % / Redundancy: 3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.104 / Rrim(I) all: 0.151 / Net I/σ(I): 5.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2267 / CC1/2: 0.576 / Rpim(I) all: 0.468 / Rrim(I) all: 0.619 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WKO

2wko


Resolution: 1.4→48.609 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.46 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2249 2551 5.189 %
Rwork0.2029 46614 -
all0.204 --
obs-49165 99.377 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.144 Å20 Å2-0.432 Å2
2---1.079 Å20 Å2
3---0.153 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 40 229 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132294
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172092
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6553104
X-RAY DIFFRACTIONr_angle_other_deg1.5611.6024838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37124.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415358
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg29.792151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.177158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022690
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02478
X-RAY DIFFRACTIONr_nbd_refined0.1910.2403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22066
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21140
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2115
X-RAY DIFFRACTIONr_metal_ion_refined0.3940.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.218
X-RAY DIFFRACTIONr_nbd_other0.2130.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.216
X-RAY DIFFRACTIONr_mcbond_it1.0491.3641225
X-RAY DIFFRACTIONr_mcbond_other1.0491.3641226
X-RAY DIFFRACTIONr_mcangle_it1.7192.0451530
X-RAY DIFFRACTIONr_mcangle_other1.7162.0441530
X-RAY DIFFRACTIONr_scbond_it1.8031.6141069
X-RAY DIFFRACTIONr_scbond_other1.8021.6161070
X-RAY DIFFRACTIONr_scangle_it2.7492.3231571
X-RAY DIFFRACTIONr_scangle_other2.7482.3251572
X-RAY DIFFRACTIONr_lrange_it4.12726.8659802
X-RAY DIFFRACTIONr_lrange_other3.98126.4949603
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.054525
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079950.0501
12FX-RAY DIFFRACTIONLocal ncs0.079950.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2821730.2823281X-RAY DIFFRACTION94.4748
1.436-1.4760.2741530.2663384X-RAY DIFFRACTION99.5217
1.476-1.5180.2572200.2433204X-RAY DIFFRACTION99.4482
1.518-1.5650.2391860.2253176X-RAY DIFFRACTION99.8219
1.565-1.6160.2031670.2163069X-RAY DIFFRACTION99.9074
1.616-1.6730.2311750.2072953X-RAY DIFFRACTION99.5544
1.673-1.7360.2511610.192875X-RAY DIFFRACTION99.8028
1.736-1.8070.2471350.1962782X-RAY DIFFRACTION99.9657
1.807-1.8870.21390.1772657X-RAY DIFFRACTION99.6081
1.887-1.9790.2131270.1792551X-RAY DIFFRACTION99.8509
1.979-2.0860.211260.1892429X-RAY DIFFRACTION99.9218
2.086-2.2130.2051320.1842281X-RAY DIFFRACTION99.7107
2.213-2.3660.2081250.1782154X-RAY DIFFRACTION99.7811
2.366-2.5550.187890.1922020X-RAY DIFFRACTION99.9526
2.555-2.7980.2261160.2041848X-RAY DIFFRACTION99.9491
2.798-3.1280.229910.2051675X-RAY DIFFRACTION99.8869
3.128-3.610.2111030.1961455X-RAY DIFFRACTION100
3.61-4.4190.221580.2011270X-RAY DIFFRACTION99.7746
4.419-6.2360.24500.211985X-RAY DIFFRACTION99.615
6.236-48.6090.301250.24565X-RAY DIFFRACTION100

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