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- PDB-8ccx: Human SOD1 in complex with S-XL6 cross-linker -

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Basic information

Entry
Database: PDB / ID: 8ccx
TitleHuman SOD1 in complex with S-XL6 cross-linker
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 / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / regulation of GTPase activity / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / ectopic germ cell programmed cell death / regulation of multicellular organism growth / neuronal action potential / response to axon injury / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / determination of adult lifespan / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / 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 / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / butane-1,4-dithiol / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.665 Å
AuthorsAntonyuk, S.V. / Hossain, A. / Agar, J.N. / Hasnain, S.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)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
DepositionJan 27, 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
Revision 1.2Oct 23, 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)32,69912
Polymers31,9182
Non-polymers78110
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-130 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.810, 68.020, 50.690
Angle α, β, γ (deg.)90.000, 105.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AF

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 6 types, 282 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UDI / butane-1,4-dithiol / 1,2-dithiane 1-oxide (reacted)


Mass: 122.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 2.5M ammonium sulphate, 150mM NaCl, sodium acetate 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 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.665→37.362 Å / Num. obs: 28274 / % possible obs: 95.2 % / Redundancy: 3.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.133 / Rrim(I) all: 0.197 / Net I/σ(I): 83.8
Reflection shellResolution: 1.67→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.417 / Num. unique obs: 1412 / CC1/2: 0.757 / Rpim(I) all: 0.399 / Rrim(I) all: 0.578

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C9V

2c9v


Resolution: 1.665→37.362 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.161 / SU B: 2.531 / SU ML: 0.084 / Average fsc free: 0.9052 / Average fsc work: 0.9266 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 1400 4.952 %
Rwork0.1841 26870 -
all0.186 --
obs-28270 95.073 %
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: 19.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.054 Å2-0 Å20.233 Å2
2---0.359 Å2-0 Å2
3---0.149 Å2
Refinement stepCycle: LAST / Resolution: 1.665→37.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 26 272 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132335
X-RAY DIFFRACTIONr_bond_other_d0.010.0162189
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6293154
X-RAY DIFFRACTIONr_angle_other_deg1.4391.6015096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6885315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77124.63108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95515397
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.544152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.865158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2260.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22107
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21096
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2169
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.220
X-RAY DIFFRACTIONr_nbd_other0.2340.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2840.222
X-RAY DIFFRACTIONr_mcbond_it1.661.8461235
X-RAY DIFFRACTIONr_mcbond_other1.661.8461234
X-RAY DIFFRACTIONr_mcangle_it2.4122.7661543
X-RAY DIFFRACTIONr_mcangle_other2.4112.7651544
X-RAY DIFFRACTIONr_scbond_it2.1842.1141100
X-RAY DIFFRACTIONr_scbond_other2.1832.1141101
X-RAY DIFFRACTIONr_scangle_it3.2933.0531605
X-RAY DIFFRACTIONr_scangle_other3.2923.0541606
X-RAY DIFFRACTIONr_lrange_it5.05623.8062523
X-RAY DIFFRACTIONr_lrange_other4.8623.2672470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.665-1.7080.356910.3141936X-RAY DIFFRACTION92.939
1.708-1.7550.3081270.241861X-RAY DIFFRACTION93.1584
1.755-1.8060.2861030.1971839X-RAY DIFFRACTION93.8164
1.806-1.8610.238810.1861797X-RAY DIFFRACTION93.2936
1.861-1.9220.23870.1741751X-RAY DIFFRACTION94.5473
1.922-1.990.247910.1791709X-RAY DIFFRACTION94.8367
1.99-2.0650.198850.1841699X-RAY DIFFRACTION96.2763
2.065-2.1490.253880.1821594X-RAY DIFFRACTION96.445
2.149-2.2450.27760.1751545X-RAY DIFFRACTION96.2018
2.245-2.3540.198710.1751349X-RAY DIFFRACTION88.5839
2.354-2.4810.199730.1711254X-RAY DIFFRACTION86.0013
2.481-2.6310.242550.171366X-RAY DIFFRACTION98.0676
2.631-2.8130.227670.171293X-RAY DIFFRACTION98.9091
2.813-3.0380.261780.1711177X-RAY DIFFRACTION98.7411
3.038-3.3270.212620.171094X-RAY DIFFRACTION99.0574
3.327-3.7190.176510.1741012X-RAY DIFFRACTION99.3458
3.719-4.2920.203470.162900X-RAY DIFFRACTION99.0586
4.292-5.2510.227390.166746X-RAY DIFFRACTION99.3671
5.251-7.4040.296160.241608X-RAY DIFFRACTION99.2051

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