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- PDB-7xx3: Crystal structure of human Superoxide Dismutase (SOD1) in complex... -

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Basic information

Entry
Database: PDB / ID: 7xx3
TitleCrystal structure of human Superoxide Dismutase (SOD1) in complex with a fungal metabolite molecule, Phialomustin B (PB)
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Superoxide dismutase / protein aggregation / modulator / toxic trimer
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 / 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 / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / 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 / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / 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 / regulation of multicellular organism growth / neuronal action potential / response to axon injury / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / 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 / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / 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 / intracellular iron ion homeostasis / response to ethanol / 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
Chem-I2G / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPadmanabhan, B. / Unni, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical ResearchIndian Council of Medical Research (ICMR), India
Department of Science & Technology (DST, India)DST-FIST: SR/FST/LS-I/2017(C) India
CitationJournal: To Be Published
Title: Phialomustin-B a fungal metabolite isolated from Phialophora mustea modulates Superoxide Dismutase 1 (SOD1) aggregation: Therapeutic potential in Amyotrophic lateral sclerosis (ALS)
Authors: Unni, S. / Padmanabhan, B.
History
DepositionMay 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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]
B: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,83529
Polymers190,92210
Non-polymers1,91219
Water21,7621208
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8809
Polymers38,1842
Non-polymers6957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area14120 Å2
MethodPISA
2
D: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8007
Polymers38,1842
Non-polymers6155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area14230 Å2
MethodPISA
3
H: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3935
Polymers38,1842
Non-polymers2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-12 kcal/mol
Surface area13860 Å2
MethodPISA
4
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3154
Polymers38,1842
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-12 kcal/mol
Surface area13930 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4464
Polymers38,1842
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.445, 242.445, 144.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 10 molecules ABDCHEFGIJ

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


Mass: 19092.219 Da / Num. of mol.: 10
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 , 5 types, 1227 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-I2G / (2~{E},4~{E},6~{S})-4,6-dimethyldeca-2,4-dienoic acid


Mass: 196.286 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H20O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 1208 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3 M Sodium citrate (pH = 6.5)

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 195483 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 27.66 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.036 / Rrim(I) all: 0.117 / Χ2: 1.048 / Net I/σ(I): 7 / Num. measured all: 1880644
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.938.21.6496520.7190.5921.7470.575100
1.93-1.978.21.36796720.820.4931.4550.586100
1.97-2.018.21.05396760.8580.381.1210.585100
2.01-2.058.20.87396580.8940.3150.930.612100
2.05-2.098.20.69296760.9230.250.7360.628100
2.09-2.148.20.58496780.9410.2110.6220.638100
2.14-2.198.20.50497230.9530.1820.5370.639100
2.19-2.258.20.43596580.9610.1570.4630.655100
2.25-2.328.20.36397320.9740.1310.3870.662100
2.32-2.398.30.29396900.9820.1060.3120.688100
2.39-2.488.40.27497260.9820.0990.2920.69399.9
2.48-2.588.60.2397190.9880.0820.2440.711100
2.58-2.78.90.1997570.990.0670.2020.738100
2.7-2.849.40.15497790.9940.0520.1630.834100
2.84-3.0210.20.12897740.9960.0410.1351.034100
3.02-3.2511.40.11498190.9960.0350.1191.528100
3.25-3.5812.70.10898450.9960.0310.1122.211100
3.58-4.0913.50.08598890.9980.0240.0882.285100
4.09-5.1613.60.05199940.9990.0150.0531.331100
5.16-50130.041103660.9990.0120.0431.17599.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YTO

5yto


Resolution: 1.9→38.69 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 9830 5.04 %
Rwork0.1985 185035 -
obs0.2001 194865 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.16 Å2 / Biso mean: 33.4739 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 1.9→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10906 0 99 1216 12221
Biso mean--49 42.68 -
Num. residues----1506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.36763270.3255935626297
1.92-1.940.3583450.31286065641099
1.94-1.960.31053200.27956080640099
1.96-1.990.29833300.26726097642799
1.99-2.010.26663030.24156102640599
2.01-2.040.27293310.230860936424100
2.04-2.070.23513250.220460956420100
2.07-2.10.25352970.225261326429100
2.1-2.130.2443320.220361326464100
2.13-2.170.27293060.220661606466100
2.17-2.210.25463320.226361126444100
2.21-2.250.26393170.229761336450100
2.25-2.290.25043160.224461566472100
2.29-2.340.24233530.223460686421100
2.34-2.390.26393330.220561366469100
2.39-2.440.30043230.227961626485100
2.44-2.50.27263280.229861246452100
2.5-2.570.25963380.222461506488100
2.57-2.650.25833380.222761306468100
2.65-2.730.24973290.217362066535100
2.73-2.830.25353360.221461676503100
2.83-2.940.26633220.21362276549100
2.94-3.080.24552960.202961976493100
3.08-3.240.20553240.187462286552100
3.24-3.440.21543150.18562376552100
3.44-3.710.22253530.172461896542100
3.71-4.080.20223310.156862516582100
4.08-4.670.16923240.15076290661499
4.67-5.880.17893410.160563616702100
5.88-38.690.20843650.196266206985100

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