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- PDB-7nxx: Structure of Superoxide Dismutase 1 (SOD1) in complex with nanobo... -

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Basic information

Entry
Database: PDB / ID: 7nxx
TitleStructure of Superoxide Dismutase 1 (SOD1) in complex with nanobody 2 (Nb2).
Components
  • Superoxide dismutase [Cu-Zn]
  • nanobody 2Single-domain antibody
KeywordsMETAL BINDING PROTEIN / Cu/Zn superoxide dismutase metalloenzyme binding catalysing the dismutation of superoxides into hydrogen peroxide
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 / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / 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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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: 2.189 Å
AuthorsGallardo, R. / Rousseau, F. / Schymkowitz, J. / Ulens, C.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0C1319N Belgium
KU LeuvenC14/17/093 Belgium
Research Foundation - Flanders (FWO)G0H1716N Belgium
KU LeuvenC24/17/075 Belgium
CitationJournal: To Be Published
Title: Identification and rational improvement of a nanobody that suppresses aggregation of mutant SOD1
Authors: van der Kant, R. / Gallardo, R. / Michiels, E. / Wilkinson, H. / Claes, F. / Laird, A. / Van Den Bosch, L. / Robberecht, W. / Ghassabeh, G.H. / Oliveberg, M. / Ulens, C. / Schymkowitz, J. / Rousseau, F.
History
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7094
Polymers30,5802
Non-polymers1292
Water0
1
A: Superoxide dismutase [Cu-Zn]
B: nanobody 2
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4188
Polymers61,1604
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)115.830, 115.830, 83.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 15827.561 Da / Num. of mol.: 1
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 nanobody 2 / Single-domain antibody


Mass: 14752.282 Da / Num. of mol.: 1
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 / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 273 K / Method: vapor diffusion / Details: 0.1 M Hepes,1.5 M Lithium sulphate, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97923 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.189→58.57 Å / Num. obs: 29792 / % possible obs: 99.1 % / Redundancy: 12.8 % / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 2.19→2.26 Å / Num. unique obs: 2455 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v0a

2v0a


Resolution: 2.189→57.915 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1008 5.02 %
Rwork0.202 19083 -
obs0.2042 20091 67.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.23 Å2 / Biso mean: 53.2605 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 2.189→57.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 2 0 2145
Biso mean--47.58 --
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072189
X-RAY DIFFRACTIONf_angle_d0.9152962
X-RAY DIFFRACTIONf_chiral_restr0.057314
X-RAY DIFFRACTIONf_plane_restr0.006396
X-RAY DIFFRACTIONf_dihedral_angle_d14.2731281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1894-2.30480.4727390.355376719
2.3048-2.44920.3542810.3208148337
2.4492-2.63840.31081030.302210052
2.6384-2.90390.33141560.3024275169
2.9039-3.3240.28812040.265361189
3.324-4.18770.25592150.18714084100
4.1877-57.9150.17042100.1444287100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.412-0.03970.16090.49660.10950.14120.1011-0.2236-0.67770.32470.1841-0.40720.30910.15770.34660.35160.0899-0.31540.24390.04290.804549.023572.660134.5554
20.3833-0.55140.08410.844-0.24140.3196-0.0109-0.04630.17390.1535-0.1249-0.3322-0.06790.07430.00030.363-0.004-0.12590.2638-0.01050.138725.214747.706226.446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:153)A1 - 153
2X-RAY DIFFRACTION2(chain B and resseq 1:136)B1 - 136

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