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- PDB-7fb9: Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) -

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Basic information

Entry
Database: PDB / ID: 7fb9
TitleCrystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Superoxide / oxidation / metalloprotein / hydrogen peroxide / filament / ALS
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
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaek, Y. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Structural analysis of the overoxidized Cu/Zn-superoxide dismutase in ROS-induced ALS filament formation.
Authors: Baek, Y. / Woo, T.G. / Ahn, J. / Lee, D. / Kwon, Y. / Park, B.J. / Ha, N.C.
History
DepositionJul 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,18934
Polymers233,89214
Non-polymers1,29720
Water1267
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5444
Polymers33,4132
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,4132
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6716
Polymers33,4132
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7722
Polymers16,7071
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
N: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7722
Polymers16,7071
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.430, 112.430, 209.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
DetailsChain M and N seem to be abnormal monomer SOD1. Some of the SOD1 proteins seem to be partially disordered, and cannot make a dimer in the soluble state. The chain M or N is a partially disordered protein and attached to the normal protein complexes. As a result, they have weak and diffused electron density maps and they don't have dimeric partners.

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Components

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


Mass: 16706.570 Da / Num. of mol.: 14
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate-HCl (pH 4.5), 21% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.24
ReflectionResolution: 2.7→50 Å / Num. obs: 76247 / % possible obs: 93.8 % / Redundancy: 4.9 % / CC1/2: 0.944 / CC star: 0.986 / Rpim(I) all: 0.067 / Χ2: 0.953 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 3.083 / Num. unique obs: 3191 / CC1/2: 0.416 / CC star: 0.767 / Rpim(I) all: 0.157 / Rrim(I) all: 0.294

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PU0

1pu0


Resolution: 2.7→49.52 Å / Cross valid method: FREE R-VALUE / σ(F): 1101.29 / Phase error: 32.1254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 3946 5.27 %
Rwork0.2303 70922 -
obs0.2316 74868 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.74 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13998 0 20 7 14025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001414242
X-RAY DIFFRACTIONf_angle_d0.34719206
X-RAY DIFFRACTIONf_chiral_restr0.04382114
X-RAY DIFFRACTIONf_plane_restr0.00162601
X-RAY DIFFRACTIONf_dihedral_angle_d4.08481981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.30311170.2682581X-RAY DIFFRACTION63.59
2.75-2.80.27051430.26352809X-RAY DIFFRACTION69.19
2.8-2.850.31531410.25882927X-RAY DIFFRACTION72.72
2.85-2.910.26831350.25373282X-RAY DIFFRACTION80.21
2.91-2.970.27721970.24853325X-RAY DIFFRACTION82.14
2.97-3.040.28522240.25233538X-RAY DIFFRACTION85.77
3.04-3.120.24681470.24043582X-RAY DIFFRACTION89.44
3.12-3.20.24651980.23413694X-RAY DIFFRACTION90.21
3.2-3.30.25641770.22533684X-RAY DIFFRACTION91.44
3.3-3.40.24791890.22863743X-RAY DIFFRACTION92.03
3.4-3.520.26291880.22213790X-RAY DIFFRACTION92.82
3.52-3.660.23082280.21223677X-RAY DIFFRACTION90.86
3.66-3.830.26691950.21523809X-RAY DIFFRACTION93.7
3.83-4.030.23712140.21833821X-RAY DIFFRACTION94.09
4.03-4.280.23811810.21363862X-RAY DIFFRACTION95.19
4.29-4.620.23032340.21093789X-RAY DIFFRACTION93.53
4.62-5.080.20641810.21363838X-RAY DIFFRACTION94.09
5.08-5.810.24692110.2353757X-RAY DIFFRACTION92.61
5.81-7.320.24292020.24083828X-RAY DIFFRACTION94.4
7.32-49.520.24952170.2623813X-RAY DIFFRACTION93.59

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