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- PDB-8k33: SOD1 and Nanobody1 complex -

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Basic information

Entry
Database: PDB / ID: 8k33
TitleSOD1 and Nanobody1 complex
Components
  • NB1
  • 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 and Nanobody1 complex
Authors: Cheng, S.
History
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: NB1
C: Superoxide dismutase [Cu-Zn]
D: NB1
E: Superoxide dismutase [Cu-Zn]
F: NB1
G: Superoxide dismutase [Cu-Zn]
H: NB1
I: Superoxide dismutase [Cu-Zn]
J: NB1
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
M: NB1
N: Superoxide dismutase [Cu-Zn]
O: NB1
P: Superoxide dismutase [Cu-Zn]
Q: NB1
R: NB1
Y: Superoxide dismutase [Cu-Zn]
T: NB1
U: Superoxide dismutase [Cu-Zn]
V: NB1
W: Superoxide dismutase [Cu-Zn]
X: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,45936
Polymers340,67424
Non-polymers78512
Water21,4021188
1
A: Superoxide dismutase [Cu-Zn]
B: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
D: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase [Cu-Zn]
F: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase [Cu-Zn]
H: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Superoxide dismutase [Cu-Zn]
J: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Superoxide dismutase [Cu-Zn]
Q: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
L: Superoxide dismutase [Cu-Zn]
M: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
N: Superoxide dismutase [Cu-Zn]
O: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
P: Superoxide dismutase [Cu-Zn]
R: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
Y: Superoxide dismutase [Cu-Zn]
T: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Superoxide dismutase [Cu-Zn]
V: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Superoxide dismutase [Cu-Zn]
X: NB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4553
Polymers28,3902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.208, 119.670, 130.707
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15827.561 Da / Num. of mol.: 12
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: 12561.965 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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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: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.13→112.16 Å / Num. obs: 180626 / % possible obs: 93.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 10.5
Reflection shellResolution: 2.13→2.24 Å / Rmerge(I) obs: 0.693 / Num. unique obs: 27136

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Processing

Software
NameVersionClassification
PHENIX(1.20.1)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→112.16 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 8939 4.96 %
Rwork0.2167 --
obs0.2191 180393 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→112.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23696 0 12 1188 24896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.601
X-RAY DIFFRACTIONf_dihedral_angle_d5.0633384
X-RAY DIFFRACTIONf_chiral_restr0.0473540
X-RAY DIFFRACTIONf_plane_restr0.0044391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.150.40073260.32746057X-RAY DIFFRACTION99
2.15-2.180.36593010.316065X-RAY DIFFRACTION99
2.18-2.20.36323120.2956067X-RAY DIFFRACTION100
2.2-2.230.37613320.3096083X-RAY DIFFRACTION99
2.23-2.240.4087760.36451471X-RAY DIFFRACTION74
2.26-2.290.38142310.29365107X-RAY DIFFRACTION85
2.29-2.320.34443030.27426097X-RAY DIFFRACTION100
2.32-2.360.31493160.26756068X-RAY DIFFRACTION99
2.36-2.40.34753200.26466107X-RAY DIFFRACTION100
2.4-2.430.33383250.26366076X-RAY DIFFRACTION100
2.43-2.480.3033520.26016024X-RAY DIFFRACTION100
2.48-2.520.32933410.2566090X-RAY DIFFRACTION100
2.52-2.570.33973360.266109X-RAY DIFFRACTION100
2.57-2.620.34193200.27736071X-RAY DIFFRACTION100
2.62-2.650.40691080.32912352X-RAY DIFFRACTION89
2.69-2.740.3262340.27284351X-RAY DIFFRACTION91
2.74-2.810.32823130.25226113X-RAY DIFFRACTION100
2.81-2.890.3323340.25646076X-RAY DIFFRACTION100
2.89-2.970.26952910.23916119X-RAY DIFFRACTION99
2.97-3.070.27563060.23636095X-RAY DIFFRACTION99
3.07-3.180.2723270.22626046X-RAY DIFFRACTION99
3.18-3.30.2643200.22326121X-RAY DIFFRACTION99
3.3-3.450.25722780.2146054X-RAY DIFFRACTION98
3.45-3.640.24273010.20236063X-RAY DIFFRACTION98
3.64-3.860.24412850.19546111X-RAY DIFFRACTION99
3.86-4.160.21563140.17616049X-RAY DIFFRACTION99
4.16-4.580.20613200.16276000X-RAY DIFFRACTION98
4.58-5.240.21033100.1646130X-RAY DIFFRACTION99
5.24-6.610.25123740.18946126X-RAY DIFFRACTION99
6.61-112.160.17743330.17126156X-RAY DIFFRACTION98

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