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- PDB-9mil: Superoxide dismutase residues 28-39 with G37R mutation -

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Basic information

Entry
Database: PDB / ID: 9mil
TitleSuperoxide dismutase residues 28-39 with G37R mutation
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsPROTEIN FIBRIL / Corkescrew / amyloid oligomer
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 / zinc ion binding / extracellular region / 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
DI(HYDROXYETHYL)ETHER / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSawaya, M.R. / Hirschbeck, S.S. / Eisenberg, D.S. / Do, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01AG070895-01A1 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Amyloid Oligomers: Expediting Crystal Growth and Revisiting the Corkscrew Structures.
Authors: Hirschbeck, S.S. / Sawaya, M.R. / Lindberg, E.T. / Limbach, M.N. / Jang, J.H. / Lazar Cantrell, K.L. / Eisenberg, D.S. / Do, T.D.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,84218
Polymers13,86710
Non-polymers9758
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.890, 59.890, 93.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 28 through 36)
d_2ens_1(chain "C" and resid 28 through 36)
d_3ens_1(chain "E" and resid 28 through 36)
d_4ens_1(chain "G" and resid 28 through 36)
d_5ens_1(chain "I" and resid 28 through 36)
d_1ens_2(chain "B" and resid 28 through 36)
d_2ens_2(chain "D" and resid 28 through 36)
d_3ens_2(chain "F" and resid 28 through 36)
d_4ens_2(chain "H" and resid 28 through 36)
d_5ens_2(chain "J" and resid 28 through 36)

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 28 - 36 / Label seq-ID: 1 - 9

Dom-IDEns-IDAuth asym-IDLabel asym-ID
d_1ens_1AA
d_2ens_1CC
d_3ens_1EE
d_4ens_1GG
d_5ens_1II
d_1ens_2BB
d_2ens_2DD
d_3ens_2FF
d_4ens_2HH
d_5ens_2JJ

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.81810023081, 0.0172297057759, -0.574817492416), (-0.211535401485, 0.938488016557, -0.272934088559), (0.534756754297, 0.344881689885, 0.771421955687)11.9079658544, 14.4861411219, -8.86924356049
2given(0.18421863994, -0.300985095307, -0.935666321453), (-0.51300705287, 0.782560026869, -0.35273725073), (0.838383716686, 0.544984198624, -0.01024533288)31.0582253036, 28.0761634257, -3.32834022614
3given(-0.385663912587, -0.644109864804, -0.660595056437), (-0.746914651464, 0.638287293338, -0.186300388062), (0.541647348333, 0.421558789761, -0.727259470078)38.1763628949, 36.4294081852, 15.4234880902
4given(-0.489433831201, -0.832911497981, -0.258288523567), (-0.852267911371, 0.519588104124, -0.0605607901234), (0.184645422697, 0.190490520981, -0.964167739189)32.3686854323, 43.0082299991, 27.087904641
5given(0.750158386826, -0.0561708089204, -0.658868146825), (-0.173285062185, 0.944866554611, -0.277847946188), (0.638149419728, 0.322601974889, 0.699066008256)14.4299182634, 13.6103507292, -11.0656849605
6given(0.182326823214, -0.271806979073, -0.944922163812), (-0.477586188799, 0.815564888961, -0.326749665894), (0.859458179206, 0.510857003496, 0.0188880961043)32.2241376447, 27.3171303541, -5.36789775379
7given(-0.381268528803, -0.649775223686, -0.657591413895), (-0.720130738009, 0.654790774724, -0.229479326978), (0.579694772375, 0.386058544809, -0.717574226726)37.5533499336, 36.7936512662, 13.2953396931
8given(-0.555174036488, -0.796683539474, -0.238908198146), (-0.806854308395, 0.585601092995, -0.0778298458648), (0.20191065904, 0.149554999297, -0.967918068822)34.4378159624, 44.162027841, 25.1793061136

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Components

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


Mass: 1386.704 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.51 Å3/Da / Density % sol: 65 % / Description: thick hexagonal plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→19.6 Å / Num. obs: 7087 / % possible obs: 99.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 76.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.129 / Net I/σ(I): 10.03
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.561.8354930.351.9631
2.56-2.631.7375000.4461.8581
2.63-2.711.3725040.5871.4591
2.71-2.791.0124620.7111.0771
2.79-2.880.8024730.7620.8551
2.88-2.980.5564520.8980.5931
2.98-3.10.364170.9390.3841
3.1-3.220.2674270.9650.2861
3.22-3.370.2364000.980.2541
3.37-3.530.1913840.9810.2071
3.53-3.720.1833600.9810.1971
3.72-3.950.1293400.990.1391
3.95-4.220.1073360.990.1151
4.22-4.560.0933080.9940.11
4.56-4.990.0882950.9950.0941
4.99-5.580.0862560.9940.0921
5.58-6.450.092320.9910.0971
6.45-7.90.0792070.9910.0861
7.9-11.170.0631610.9990.0691
11.17-19.60.058800.9960.0641

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XSCALE20220820data scaling
XDS20220820data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.6 Å / SU ML: 0.4045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 709 10.01 %
Rwork0.2187 6376 -
obs0.2231 7085 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 58 11 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421050
X-RAY DIFFRACTIONf_angle_d0.68171397
X-RAY DIFFRACTIONf_chiral_restr0.062160
X-RAY DIFFRACTIONf_plane_restr0.0044140
X-RAY DIFFRACTIONf_dihedral_angle_d13.7031404
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.16013385867
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.904171500083
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.21670148224
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS1.54422206447
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.04831399398
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS1.20386726995
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS1.38598078665
ens_2d_5BBX-RAY DIFFRACTIONTorsion NCS1.75080390407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.39761370.34981236X-RAY DIFFRACTION99.56
2.69-2.960.39591380.32621241X-RAY DIFFRACTION100
2.96-3.390.28931420.22471274X-RAY DIFFRACTION100
3.39-4.250.28361410.20841274X-RAY DIFFRACTION99.37
4.26-19.60.21921510.19851351X-RAY DIFFRACTION99.87

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