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- PDB-8yaf: SOD1, Nanobody1 and Nanobody2 complex -

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Basic information

Entry
Database: PDB / ID: 8yaf
TitleSOD1, Nanobody1 and Nanobody2 complex
Components
  • NB1
  • NB2
  • Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / antibody complex / OXIDOREDUCTASE / OXIDOREDUCTASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / 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 / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / 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 phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsCheng, S.
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, Nanobody1 and Nanobody2 complex
Authors: Cheng, S.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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: NB1
C: NB2
D: Superoxide dismutase [Cu-Zn]
E: NB1
F: NB2
H: Superoxide dismutase [Cu-Zn]
I: NB1
J: NB2
L: Superoxide dismutase [Cu-Zn]
M: NB1
N: NB2
P: Superoxide dismutase [Cu-Zn]
Q: NB1
R: NB2
T: Superoxide dismutase [Cu-Zn]
U: NB1
V: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,75924
Polymers255,36718
Non-polymers3926
Water00
1
A: Superoxide dismutase [Cu-Zn]
B: NB1
C: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Superoxide dismutase [Cu-Zn]
E: NB1
F: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Superoxide dismutase [Cu-Zn]
I: NB1
J: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L: Superoxide dismutase [Cu-Zn]
M: NB1
N: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
P: Superoxide dismutase [Cu-Zn]
Q: NB1
R: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
T: Superoxide dismutase [Cu-Zn]
U: NB1
V: NB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5613
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.949, 218.892, 122.708
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: 15827.561 Da / Num. of mol.: 6
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
NB1


Mass: 12649.041 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Protein
NB2


Mass: 14084.497 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 5% (v/v) Isopropanol, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.28→117.91 Å / Num. obs: 58709 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.084 / Rrim(I) all: 0.269 / Χ2: 1 / Net I/σ(I): 8.8 / Num. measured all: 598758
Reflection shellResolution: 3.28→3.45 Å / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 1.034 / Num. measured all: 89071 / Num. unique obs: 8449 / CC1/2: 0.84 / Rpim(I) all: 0.334 / Rrim(I) all: 1.087 / Χ2: 0.97 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→81.68 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1997 3.41 %
Rwork0.1996 --
obs0.2013 58593 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.28→81.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17756 0 6 0 17762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.321
X-RAY DIFFRACTIONf_dihedral_angle_d6.762571
X-RAY DIFFRACTIONf_chiral_restr0.0662614
X-RAY DIFFRACTIONf_plane_restr0.0113284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.360.31171400.27473964X-RAY DIFFRACTION100
3.36-3.450.33191410.26324020X-RAY DIFFRACTION100
3.45-3.550.32141410.24343978X-RAY DIFFRACTION100
3.55-3.660.28011420.22384000X-RAY DIFFRACTION100
3.66-3.80.26471410.22343999X-RAY DIFFRACTION100
3.8-3.950.27331410.21144010X-RAY DIFFRACTION100
3.95-4.130.21761410.18814030X-RAY DIFFRACTION100
4.13-4.350.24961410.18114010X-RAY DIFFRACTION100
4.35-4.620.2071420.16174023X-RAY DIFFRACTION100
4.62-4.970.22511440.16764053X-RAY DIFFRACTION100
4.97-5.470.23511430.17884058X-RAY DIFFRACTION100
5.47-6.270.22791440.19844091X-RAY DIFFRACTION100
6.27-7.890.25771460.20324116X-RAY DIFFRACTION100
7.89-81.680.22341500.19194244X-RAY DIFFRACTION98

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