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- PDB-7t8e: G93A mutant of human SOD1 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 7t8e
TitleG93A mutant of human SOD1 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 / placenta development / response to amphetamine / 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 / negative regulation of inflammatory response / small GTPase binding / 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
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.3Oct 9, 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)32,1969
Polymers31,6832
Non-polymers5137
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-133 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.740, 68.210, 51.080
Angle α, β, γ (deg.)90.000, 105.630, 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: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

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-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.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 40.04 %
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→49.24 Å / Num. obs: 50157 / % possible obs: 99.6 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2482 / CC1/2: 0.563 / % possible all: 99.2

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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→49.24 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.484 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.229 2598 5.18 %
Rwork0.1987 47559 -
all0.2 --
obs-50157 99.549 %
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: 18.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å2-0 Å20.07 Å2
2---0.85 Å2-0 Å2
3---0.674 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 18 240 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172064
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6373093
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5914781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39624.423104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83515353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.369158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
X-RAY DIFFRACTIONr_nbd_refined0.1840.2390
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21945
X-RAY DIFFRACTIONr_nbtor_refined0.1490.21064
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2142
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.215
X-RAY DIFFRACTIONr_nbd_other0.2120.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.215
X-RAY DIFFRACTIONr_mcbond_it1.3011.8281229
X-RAY DIFFRACTIONr_mcbond_other1.291.8281228
X-RAY DIFFRACTIONr_mcangle_it2.0192.7391533
X-RAY DIFFRACTIONr_mcangle_other2.0192.7391534
X-RAY DIFFRACTIONr_scbond_it2.112.0541049
X-RAY DIFFRACTIONr_scbond_other2.0962.041041
X-RAY DIFFRACTIONr_scangle_it3.2362.9811557
X-RAY DIFFRACTIONr_scangle_other3.2392.9581545
X-RAY DIFFRACTIONr_lrange_it4.64536.0099615
X-RAY DIFFRACTIONr_lrange_other4.50835.5549386
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.054462
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.096490.0501
12FX-RAY DIFFRACTIONLocal ncs0.096490.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.341930.3483524X-RAY DIFFRACTION99.3585
1.436-1.4760.3291470.33436X-RAY DIFFRACTION99.8885
1.476-1.5180.2662260.2643286X-RAY DIFFRACTION99.8862
1.518-1.5650.281890.2433225X-RAY DIFFRACTION99.9707
1.565-1.6160.251760.2283157X-RAY DIFFRACTION99.9101
1.616-1.6730.2461700.2183042X-RAY DIFFRACTION99.9689
1.673-1.7360.2741630.2092900X-RAY DIFFRACTION99.9022
1.736-1.8070.2481470.1952818X-RAY DIFFRACTION99.7645
1.807-1.8870.2491390.1922730X-RAY DIFFRACTION99.7219
1.887-1.9790.221310.1962577X-RAY DIFFRACTION99.6321
1.979-2.0860.2511220.22450X-RAY DIFFRACTION99.4202
2.086-2.2130.2461380.1942331X-RAY DIFFRACTION99.5163
2.213-2.3660.2291290.1842193X-RAY DIFFRACTION99.4007
2.366-2.5550.199860.1922033X-RAY DIFFRACTION99.065
2.555-2.7980.2511160.1971858X-RAY DIFFRACTION99.1462
2.798-3.1280.204930.1881694X-RAY DIFFRACTION98.8385
3.128-3.610.1821020.1771470X-RAY DIFFRACTION98.558
3.61-4.4190.198560.1621283X-RAY DIFFRACTION99.1118
4.419-6.2360.209520.183988X-RAY DIFFRACTION98.2987
6.236-49.240.224240.226564X-RAY DIFFRACTION98.3278

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