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- PDB-5k02: Structure of human SOD1 with T2D mutation -

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Basic information

Entry
Database: PDB / ID: 5k02
TitleStructure of human SOD1 with T2D mutation
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / Phosphomimetic Mutation
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide / regulation of GTPase activity / auditory receptor cell stereocilium organization / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / muscle cell cellular homeostasis / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / thymus development / superoxide dismutase activity / ovarian follicle development / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / transmission of nerve impulse / response to axon injury / reactive oxygen species metabolic process / placenta development / embryo implantation / positive regulation of superoxide anion generation / sensory perception of sound / response to amphetamine / axon cytoplasm / removal of superoxide radicals / positive regulation of phagocytosis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of mitochondrial membrane potential / dendrite cytoplasm / locomotory behavior / positive regulation of cytokine production / glutathione metabolic process / response to hydrogen peroxide / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / negative regulation of neuron apoptotic process / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / positive regulation of MAPK cascade / intracellular iron ion homeostasis / lysosome / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFay, J.M. / Zhu, C. / Cui, W. / Ke, H. / Dokholyan, N.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080742 United States
CitationJournal: Structure / Year: 2016
Title: A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation.
Authors: Fay, J.M. / Zhu, C. / Proctor, E.A. / Tao, Y. / Cui, W. / Ke, H. / Dokholyan, N.V.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]
O: Superoxide dismutase [Cu-Zn]
P: Superoxide dismutase [Cu-Zn]
Q: Superoxide dismutase [Cu-Zn]
R: Superoxide dismutase [Cu-Zn]
S: Superoxide dismutase [Cu-Zn]
T: Superoxide dismutase [Cu-Zn]
U: Superoxide dismutase [Cu-Zn]
V: Superoxide dismutase [Cu-Zn]
W: Superoxide dismutase [Cu-Zn]
X: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,29272
Polymers380,19724
Non-polymers3,09548
Water12,322684
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-37 kcal/mol
Surface area13810 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
hetero molecules

L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1690 Å2
ΔGint-37 kcal/mol
Surface area13780 Å2
MethodPISA
3
D: Superoxide dismutase [Cu-Zn]
hetero molecules

K: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area1710 Å2
ΔGint-36 kcal/mol
Surface area13720 Å2
MethodPISA
4
E: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-36 kcal/mol
Surface area14120 Å2
MethodPISA
5
F: Superoxide dismutase [Cu-Zn]
hetero molecules

I: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1630 Å2
ΔGint-38 kcal/mol
Surface area14020 Å2
MethodPISA
6
G: Superoxide dismutase [Cu-Zn]
hetero molecules

H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area1630 Å2
ΔGint-37 kcal/mol
Surface area14030 Å2
MethodPISA
7
M: Superoxide dismutase [Cu-Zn]
N: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-38 kcal/mol
Surface area13820 Å2
MethodPISA
8
X: Superoxide dismutase [Cu-Zn]
hetero molecules

O: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1510 Å2
ΔGint-24 kcal/mol
Surface area13790 Å2
MethodPISA
9
W: Superoxide dismutase [Cu-Zn]
hetero molecules

P: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area1470 Å2
ΔGint-24 kcal/mol
Surface area13920 Å2
MethodPISA
10
Q: Superoxide dismutase [Cu-Zn]
V: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-12 kcal/mol
Surface area13840 Å2
MethodPISA
11
R: Superoxide dismutase [Cu-Zn]
hetero molecules

U: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area13860 Å2
MethodPISA
12
S: Superoxide dismutase [Cu-Zn]
hetero molecules

T: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9416
Polymers31,6832
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area1380 Å2
ΔGint-12 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.980, 111.961, 149.880
Angle α, β, γ (deg.)89.86, 89.85, 60.13
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15841.545 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00441, superoxide dismutase
#2: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
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: 4.29 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: T2D was crystallized in a buffer of 2 M (NH4)2SO4, 0.1 M Sodium Cacodylate, 20% MPD and 10 mM ZnCl2 (pH 6.5) after a period of approximately 5 months.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→149.92 Å / Num. obs: 431865 / % possible obs: 80.41 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.061 / Net I/av σ(I): 18.333 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.142.30.543177.8
2.14-2.182.30.509177.3
2.18-2.222.40.58177.6
2.22-2.262.30.405177.3
2.26-2.312.40.469177.8
2.31-2.372.40.281177.8
2.37-2.422.40.246178.1
2.42-2.492.40.218178.4
2.49-2.562.50.195179.5
2.56-2.652.50.167178.8
2.65-2.742.50.143179
2.74-2.852.50.111179.8
2.85-2.982.50.088179.7
2.98-3.142.50.067180
3.14-3.332.50.053181
3.33-3.592.50.046183
3.59-3.952.60.043186.4
3.95-4.522.60.037193.6
4.52-5.72.80.036198.8
5.7-503.10.034198.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CU,ZN SUPEROXIDE DISMUTASE (PDB ID: 1SPD)

1spd


Resolution: 1.99→149.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.863 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16198 17889 5.2 %RANDOM
Rwork0.14611 ---
obs0.14693 329360 80.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.107 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å2-8.4 Å26.77 Å2
2---3.19 Å2-1.89 Å2
3---6.88 Å2
Refinement stepCycle: 1 / Resolution: 1.99→149.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26664 0 48 684 27396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01927288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.94536600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99253648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90825.7141176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.108154440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0251596
X-RAY DIFFRACTIONr_chiral_restr0.0740.24008
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 984 -
Rwork0.196 19832 -
obs--65.15 %

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