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- PDB-3ltv: Mouse-human sod1 chimera -

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Basic information

Entry
Database: PDB / ID: 3ltv
TitleMouse-human sod1 chimera
ComponentsSuperoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION / PHOSPHOPROTEIN
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth ...Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / 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 / 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 / regulation of protein kinase activity / response to copper ion / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / response to nutrient levels / response to reactive oxygen species / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / secretory granule / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / 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 / myelin sheath / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / response to oxidative stress / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / lysosome / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / negative regulation of apoptotic process / enzyme binding / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.453 Å
AuthorsSeetharaman, S.V. / Taylor, A.B. / Hart, P.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: Structures of mouse SOD1 and human/mouse SOD1 chimeras.
Authors: Seetharaman, S.V. / Taylor, A.B. / Holloway, S. / Hart, P.J.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 7, 2017Group: Database references / Structure summary
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,89512
Polymers94,5026
Non-polymers3926
Water2,612145
1
A: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6324
Polymers31,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-11 kcal/mol
Surface area13670 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6324
Polymers31,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area13520 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6324
Polymers31,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-10 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.480, 127.480, 102.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 15750.348 Da / Num. of mol.: 6
Fragment: RESIDUES 2-81 FROM MOUSE PROTEIN, RESIDUES 82-154 FROM HUMAN PROTEIN,RESIDUES 2-81 FROM MOUSE PROTEIN, RESIDUES 82-154 FROM HUMAN PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Sod1, SOD1 / Plasmid: PKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08228, UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M SODIUM ACETATE, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL SIDE-BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 34238 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.103 / Net I/σ(I): 14.5
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.55 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VR7

2vr7


Resolution: 2.453→37.557 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1724 5.04 %RANDOM
Rwork0.1953 ---
obs0.1988 34219 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.425 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.3397 Å20 Å20 Å2
2--2.3397 Å20 Å2
3----4.2956 Å2
Refinement stepCycle: LAST / Resolution: 2.453→37.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 6 145 6742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096704
X-RAY DIFFRACTIONf_angle_d1.1789046
X-RAY DIFFRACTIONf_dihedral_angle_d19.3912381
X-RAY DIFFRACTIONf_chiral_restr0.0751000
X-RAY DIFFRACTIONf_plane_restr0.0041235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4531-2.52530.30011630.23742610X-RAY DIFFRACTION97
2.5253-2.60680.33731380.24462738X-RAY DIFFRACTION100
2.6068-2.69990.35911580.24622704X-RAY DIFFRACTION99
2.6999-2.8080.33351490.24292711X-RAY DIFFRACTION99
2.808-2.93570.31421330.2322721X-RAY DIFFRACTION99
2.9357-3.09040.31871380.22342736X-RAY DIFFRACTION99
3.0904-3.2840.29381430.20552694X-RAY DIFFRACTION99
3.284-3.53740.24281260.18942738X-RAY DIFFRACTION99
3.5374-3.8930.22561360.17612712X-RAY DIFFRACTION99
3.893-4.45550.23581510.16212689X-RAY DIFFRACTION98
4.4555-5.61050.21391540.16742712X-RAY DIFFRACTION98
5.6105-37.56140.23021350.17022730X-RAY DIFFRACTION97

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