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- PDB-5u9m: Copper-Zinc Superoxide Dismutase is Activated through a Sulfenic ... -

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Basic information

Entry
Database: PDB / ID: 5u9m
TitleCopper-Zinc Superoxide Dismutase is Activated through a Sulfenic Acid Intermediate at a Copper-ion Entry Site
Components
  • Superoxide dismutase 1 copper chaperone
  • Superoxide dismutase [Cu-Zn]
Keywordsoxidoreductase/chaperone / oxidoreductase-chaperone complex / Cu-Zn superoxide dismutase / metallochaperone
Function / homology
Function and homology information


superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / action potential initiation / copper ion transport / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth ...superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / action potential initiation / copper ion transport / 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 / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / protein folding chaperone complex / regulation of protein kinase activity / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / negative regulation of developmental process / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / removal of superoxide radicals / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / response to hydrogen peroxide / placenta development / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / 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 inner membrane / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 copper chaperone
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTaylor, A.B. / Hart, P.J. / Winkler, D.D.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site.
Authors: Fetherolf, M.M. / Boyd, S.D. / Taylor, A.B. / Kim, H.J. / Wohlschlegel, J.A. / Blackburn, N.J. / Hart, P.J. / Winge, D.R. / Winkler, D.D.
History
DepositionDec 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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 1 copper chaperone
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9267
Polymers85,7304
Non-polymers1963
Water2,162120
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9964
Polymers42,8652
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area17830 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase 1 copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9303
Polymers42,8652
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-13 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.097, 184.353, 48.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15836.590 Da / Num. of mol.: 2 / Mutation: H46R,H48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: UniProt: P00441, superoxide dismutase
#2: Protein Superoxide dismutase 1 copper chaperone


Mass: 27028.498 Da / Num. of mol.: 2 / Mutation: E238A,E239A,R240A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CCS1, LYS7, YMR038C, YM9532.03C / Plasmid: PKA6H / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40202
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25 % PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→48.51 Å / Num. obs: 38015 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 45.51 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZU,1JK9

1ozu

1jk9


Resolution: 2.35→46.917 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2349 2000 5.27 %
Rwork0.1861 --
obs0.1887 37948 99.86 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.35→46.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 3 120 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095832
X-RAY DIFFRACTIONf_angle_d1.1427886
X-RAY DIFFRACTIONf_dihedral_angle_d13.1262116
X-RAY DIFFRACTIONf_chiral_restr0.046890
X-RAY DIFFRACTIONf_plane_restr0.0051037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.32761400.26652509X-RAY DIFFRACTION100
2.4088-2.47390.29711400.26442531X-RAY DIFFRACTION100
2.4739-2.54670.31741430.24892549X-RAY DIFFRACTION100
2.5467-2.62890.28131390.23962512X-RAY DIFFRACTION100
2.6289-2.72290.27721420.23422543X-RAY DIFFRACTION100
2.7229-2.83190.30051410.21452546X-RAY DIFFRACTION100
2.8319-2.96070.27581400.23432513X-RAY DIFFRACTION100
2.9607-3.11680.28891410.22742556X-RAY DIFFRACTION100
3.1168-3.3120.25421440.20272563X-RAY DIFFRACTION100
3.312-3.56770.25441410.19312554X-RAY DIFFRACTION100
3.5677-3.92650.22281450.17132583X-RAY DIFFRACTION100
3.9265-4.49430.20981430.14522595X-RAY DIFFRACTION100
4.4943-5.66080.17971460.14642625X-RAY DIFFRACTION100
5.6608-46.9260.1941550.16462769X-RAY DIFFRACTION99

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