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- PDB-8q6m: Human SOD1 low dose data collecton -

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Basic information

Entry
Database: PDB / ID: 8q6m
TitleHuman SOD1 low dose data collecton
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / Amyotrophic Lateral Sclerosis / ALS / pharmacological chaperone / cross-linking / stabilization
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAntonyuk, S.V. / Hossain, A. / Agar, J.N. / Hasnain, S.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01NS065263 United States
National Science Foundation (NSF, United States)MCB-1517290 United States
National Science Foundation (NSF, United States)CHE-1905214 United States
CitationJournal: Plos Biol. / Year: 2024
Title: Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS.
Authors: Hossain, M.A. / Sarin, R. / Donnelly, D.P. / Miller, B.C. / Weiss, A. / McAlary, L. / Antonyuk, S.V. / Salisbury, J.P. / Amin, J. / Conway, J.B. / Watson, S.S. / Winters, J.N. / Xu, Y. / ...Authors: Hossain, M.A. / Sarin, R. / Donnelly, D.P. / Miller, B.C. / Weiss, A. / McAlary, L. / Antonyuk, S.V. / Salisbury, J.P. / Amin, J. / Conway, J.B. / Watson, S.S. / Winters, J.N. / Xu, Y. / Alam, N. / Brahme, R.R. / Shahbazian, H. / Sivasankar, D. / Padmakumar, S. / Sattarova, A. / Ponmudiyan, A.C. / Gawde, T. / Verrill, D.E. / Yang, W. / Kannapadi, S. / Plant, L.D. / Auclair, J.R. / Makowski, L. / Petsko, G.A. / Ringe, D. / Agar, N.Y.R. / Greenblatt, D.J. / Ondrechen, M.J. / Chen, Y. / Yerbury, J.J. / Manetsch, R. / Hasnain, S.S. / Brown Jr., R.H. / Agar, J.N.
History
DepositionAug 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,52310
Polymers31,9182
Non-polymers6058
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-64 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 68.010, 52.580
Angle α, β, γ (deg.)90.000, 106.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 15958.757 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 341 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 0.4 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.75 / Details: 2.5 M Ammonium sulphate, Acetate buffer pH 4.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→37.69 Å / Num. obs: 25235 / % possible obs: 97.3 % / Redundancy: 3.3 % / CC1/2: 0.974 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.125 / Rrim(I) all: 0.184 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.03-37.692.90.0885980.9880.0860.123
1.77-1.813.30.41147740.6490.3930.569

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
MAR345dtbdata collection
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→35.338 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.23 / SU B: 3.695 / SU ML: 0.118 / Average fsc free: 0.8964 / Average fsc work: 0.9001 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2505 933 3.699 %
Rwork0.2089 24287 -
all0.211 --
obs-25220 97.221 %
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: 19.766 Å2
Baniso -1Baniso -2Baniso -3
1-0.994 Å20 Å2-1.423 Å2
2---1.241 Å2-0 Å2
3---0.921 Å2
Refinement stepCycle: LAST / Resolution: 1.77→35.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 23 333 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132312
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162135
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6293126
X-RAY DIFFRACTIONr_angle_other_deg1.2721.5964959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9045313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88524.528106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81215377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.336158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022716
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
X-RAY DIFFRACTIONr_nbd_refined0.1810.2394
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21796
X-RAY DIFFRACTIONr_nbtor_refined0.1340.21030
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.229
X-RAY DIFFRACTIONr_nbd_other0.1680.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.228
X-RAY DIFFRACTIONr_mcbond_it1.5221.9121244
X-RAY DIFFRACTIONr_mcbond_other1.5181.9111243
X-RAY DIFFRACTIONr_mcangle_it2.42.8571553
X-RAY DIFFRACTIONr_mcangle_other2.42.8571554
X-RAY DIFFRACTIONr_scbond_it1.9232.1821068
X-RAY DIFFRACTIONr_scbond_other1.8862.1551056
X-RAY DIFFRACTIONr_scangle_it3.0673.1691571
X-RAY DIFFRACTIONr_scangle_other3.0313.1251553
X-RAY DIFFRACTIONr_lrange_it5.17323.9542359
X-RAY DIFFRACTIONr_lrange_other4.81523.3732294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.816200.3341846X-RAY DIFFRACTION97.0047
3.953-4.5620.197370.169772X-RAY DIFFRACTION99.8765
5.58-7.8660.314200.237525X-RAY DIFFRACTION100

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