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- PDB-1ozt: Crystal Structure of apo-H46R Familial ALS Mutant human Cu,Zn Sup... -

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Basic information

Entry
Database: PDB / ID: 1ozt
TitleCrystal Structure of apo-H46R Familial ALS Mutant human Cu,Zn Superoxide Dismutase (CuZnSOD) to 2.5A resolution
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / beta barrel / amyloid-like linear filaments
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / 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 / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsElam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Amyloid-like Filaments and Water-filled Nanotubes Formed by SOD1 Mutant Proteins Linked to Familial ALS
Authors: Elam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)126,7738
Polymers126,7738
Non-polymers00
Water4,234235
1
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6932
Polymers31,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area14200 Å2
MethodPISA
2
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6932
Polymers31,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area13220 Å2
MethodPISA
3
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6932
Polymers31,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area12050 Å2
MethodPISA
4
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6932
Polymers31,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-11 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.617, 69.998, 113.787
Angle α, β, γ (deg.)90.00, 110.37, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer. There are 4 homodimers in the asymmetric unit.

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15846.607 Da / Num. of mol.: 8 / Mutation: H46R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: P00441, superoxide dismutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium acetate, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113.8 mg/mlprotein1drop
2100 mMpotassium phosphate1droppH7.2
350 mM1dropKCl
40.2 Mmagnesium acetate1reservoir
50.1 Msodium cacodylate1reservoirpH6.5
620 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 40758 / Num. obs: 40758 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.44
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.32 / Num. unique all: 2719 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Num. measured all: 167752
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AZV

1azv


Resolution: 2.5→42.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2446069.4 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2064 5.1 %RANDOM
Rwork0.222 ---
all0.2243 40746 --
obs0.2243 40746 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9058 Å2 / ksol: 0.336112 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--14.8 Å20 Å20.41 Å2
2--29.52 Å20 Å2
3----14.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7966 0 0 235 8201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 379 5.7 %
Rwork0.343 6307 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 42.4 Å / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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