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- PDB-3cqp: Human SOD1 G85R Variant, Structure I -

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Basic information

Entry
Database: PDB / ID: 3cqp
TitleHuman SOD1 G85R Variant, Structure I
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION
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
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / MALONATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. ...Cao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Hasnain, S.S. / Hart, P.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of the G85R Variant of SOD1 in Familial Amyotrophic Lateral Sclerosis.
Authors: Cao, X. / Antonyuk, S.V. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / ...Authors: Cao, X. / Antonyuk, S.V. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Hasnain, S.S. / Hart, P.J.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,36513
Polymers63,7114
Non-polymers6559
Water6,179343
1
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0485
Polymers31,8552
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-11.3 kcal/mol
Surface area13210 Å2
MethodPISA
2
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3178
Polymers31,8552
Non-polymers4626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8.2 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.472, 116.808, 147.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-241-

HOH

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15927.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351-HSOD / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EGY118 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.37865 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37865 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 46284 / Num. obs: 46284 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.062 / Net I/σ(I): 23.37
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.39 / Num. unique all: 4606 / Rsym value: 0.369 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZV

1azv


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.08 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22326 2347 5.1 %RANDOM
Rwork0.18266 ---
all0.18467 ---
obs-43936 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 21 343 4635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214356
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9475872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0125.348187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32315718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8121518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023320
X-RAY DIFFRACTIONr_nbd_refined0.1950.21818
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2338
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.223
X-RAY DIFFRACTIONr_mcbond_it0.5421.52849
X-RAY DIFFRACTIONr_mcangle_it1.00224535
X-RAY DIFFRACTIONr_scbond_it1.53431507
X-RAY DIFFRACTIONr_scangle_it2.3444.51337
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 148 -
Rwork0.208 3168 -
obs-3168 97.67 %
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)
11.3962-0.00440.15091.7706-0.45382.3354-0.0296-0.02030.1122-0.04490.10620.0249-0.07730.0813-0.0766-0.11120.0182-0.0085-0.09020.0066-0.10717.5592123.153860.2013
21.04730.1560.47851.9043-0.38532.79610.0721-0.0505-0.00420.0768-0.09270.10770.0591-0.13530.0206-0.1191-0.0036-0.0041-0.07690.0256-0.10151.9296102.885378.8347
31.5055-0.955-0.78064.14081.44943.2006-0.01-0.24340.2330.10230.2314-0.5586-0.10480.4224-0.2214-0.0893-0.0032-0.00260.0087-0.06480.011719.8395148.72950.5314
41.23990.2101-0.70311.53420.24533.45540.03140.03120.0448-0.12370.0127-0.0577-0.0354-0.2056-0.0442-0.08640.01860.0249-0.09690.0206-0.099213.1478135.656328.1759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1532 - 153
2X-RAY DIFFRACTION2BB2 - 1532 - 153
3X-RAY DIFFRACTION3CC2 - 1532 - 153
4X-RAY DIFFRACTION4DD2 - 1532 - 153

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