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- PDB-8k3l: SOD1 and Nanobody3 complex -

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Basic information

Entry
Database: PDB / ID: 8k3l
TitleSOD1 and Nanobody3 complex
Components
  • NB3
  • Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / antibody complex / OXIDOREDUCTASE-IMMUNE SYSTEM complex
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
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
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, S. / Liu, R. / Ding, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0805200 China
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
CitationJournal: To Be Published
Title: SOD1 and Nanobody1 complex
Authors: Shihao, C.
History
DepositionJul 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: 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: NB3
C: Superoxide dismutase [Cu-Zn]
D: NB3
E: Superoxide dismutase [Cu-Zn]
F: NB3
G: Superoxide dismutase [Cu-Zn]
H: NB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,23916
Polymers118,7238
Non-polymers5168
Water6,305350
1
A: Superoxide dismutase [Cu-Zn]
B: NB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8104
Polymers29,6812
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
D: NB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8104
Polymers29,6812
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase [Cu-Zn]
F: NB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8104
Polymers29,6812
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase [Cu-Zn]
H: NB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8104
Polymers29,6812
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.214, 62.442, 314.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15827.561 Da / Num. of mol.: 4
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: Antibody
NB3


Mass: 13853.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cu
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene, glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 55961 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Χ2: 0.445 / Net I/σ(I): 3 / Num. measured all: 739399
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.3413.51.10127320.9080.9760.3081.1440.405100
2.34-2.3813.71.00927790.930.9820.2811.0480.403100
2.38-2.4313.60.97327260.9180.9780.2711.0110.40899.8
2.43-2.4813.60.77527730.950.9870.2160.8050.413100
2.48-2.5313.60.68327890.9560.9890.1910.710.42100
2.53-2.5913.50.57527600.9670.9920.1610.5980.41799.9
2.59-2.6613.40.47127140.9820.9950.1320.4890.42799.8
2.66-2.73130.4328020.9730.9930.1230.4480.433100
2.73-2.8111.70.30527420.9850.9960.0920.3190.44499.6
2.81-2.912.70.28227500.9850.9960.0810.2940.4598.7
2.9-3140.24527990.9920.9980.0680.2540.456100
3-3.12140.18228020.9950.9990.050.1890.45899.8
3.12-3.2613.90.14527890.9960.9990.040.1510.46899.9
3.26-3.4413.60.11927630.9970.9990.0330.1230.48799.6
3.44-3.6513.50.09328220.9980.9990.0260.0960.475100
3.65-3.9312.70.07828130.9980.9990.0230.0810.47599.9
3.93-4.3311.90.06127570.99910.0180.0640.47497.8
4.33-4.9513.70.05528830.99910.0150.0570.466100
4.95-6.2413.20.05829150.99910.0170.0610.45599.8
6.24-5011.60.04730510.99910.0140.0490.47399.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.07 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2717 5.03 %
Rwork0.195 --
obs0.1971 54063 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8168 0 8 350 8526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.949
X-RAY DIFFRACTIONf_dihedral_angle_d6.6231160
X-RAY DIFFRACTIONf_chiral_restr0.061212
X-RAY DIFFRACTIONf_plane_restr0.0071500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.3241300.25862476X-RAY DIFFRACTION91
2.34-2.380.31671180.25612603X-RAY DIFFRACTION93
2.38-2.430.32211420.26052532X-RAY DIFFRACTION93
2.43-2.480.34231870.2532582X-RAY DIFFRACTION95
2.48-2.540.34641370.26022574X-RAY DIFFRACTION94
2.54-2.610.3091330.24282693X-RAY DIFFRACTION96
2.61-2.680.3011250.23432656X-RAY DIFFRACTION95
2.68-2.750.30491420.23582671X-RAY DIFFRACTION97
2.75-2.840.29641320.23962730X-RAY DIFFRACTION96
2.84-2.940.33181370.2342679X-RAY DIFFRACTION98
2.94-3.060.28451630.22782681X-RAY DIFFRACTION98
3.06-3.20.29811410.21762733X-RAY DIFFRACTION99
3.2-3.370.23741200.22032806X-RAY DIFFRACTION99
3.37-3.580.23831280.1922824X-RAY DIFFRACTION99
3.58-3.860.25861360.18712825X-RAY DIFFRACTION99
3.86-4.240.18871370.15932753X-RAY DIFFRACTION97
4.24-4.860.15322010.14112784X-RAY DIFFRACTION99
4.86-6.110.19661510.15622848X-RAY DIFFRACTION99
6.11-31.070.17751570.17692896X-RAY DIFFRACTION95

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