[English] 日本語
Yorodumi
- PDB-1ozu: Crystal Structure of Familial ALS Mutant S134N of human Cu,Zn Sup... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ozu
TitleCrystal Structure of Familial ALS Mutant S134N of human Cu,Zn Superoxide Dismutase (CuZnSOD) to 1.3A resolution
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / beta barrel / amyloid-like linear filaments
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 / myeloid cell homeostasis / regulation of GTPase activity / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / dendrite cytoplasm / reactive oxygen species metabolic process / placenta development / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / negative regulation of neuron apoptotic process / gene expression / intracellular iron ion homeostasis / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsElam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Amyloid-like Filaments and Water-filled Nanotubes Formed by SOD1 Mutant Proteins Linked to Familial ALS
Authors: Elam, J.S. / Taylor, A.B. / Strange, R. / Antonyuk, S. / Doucette, P.A. / Rodriguez, J.A. / Hasnain, S.S. / Hayward, L.J. / Valentine, J.S. / Yeates, T.O. / Hart, P.J.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,1307
Polymers31,7412
Non-polymers3885
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-79 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.086, 56.457, 105.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer. There is one homodimer in asymmetric unit.

-
Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15870.586 Da / Num. of mol.: 2 / Mutation: S134N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEp 351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG103 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
210 mMMES1droppH6.5
30.2 Msodium sulfate decahydrate1reservoir
420 %(w/v)PEG33501reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→52.7 Å / Num. all: 58507 / Num. obs: 58507 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.62 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7
Reflection shellResolution: 1.3→1.38 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.86 / Num. unique all: 5121 / % possible all: 87.1
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Num. measured all: 270095 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 87.1 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AZV

1azv


Resolution: 1.3→52.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.158 / SU ML: 0.048 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.06 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19339 2945 5 %RANDOM
Rwork0.17722 ---
all0.17806 55502 --
obs0.17806 55502 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 13 247 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212034
X-RAY DIFFRACTIONr_bond_other_d0.0010.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.952739
X-RAY DIFFRACTIONr_angle_other_deg0.85434200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6433268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13815328
X-RAY DIFFRACTIONr_chiral_restr0.2820.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02365
X-RAY DIFFRACTIONr_nbd_refined0.3110.3381
X-RAY DIFFRACTIONr_nbd_other0.2250.31721
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.5237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0211.51341
X-RAY DIFFRACTIONr_mcangle_it1.76222121
X-RAY DIFFRACTIONr_scbond_it2.2583693
X-RAY DIFFRACTIONr_scangle_it3.5864.5618
X-RAY DIFFRACTIONr_rigid_bond_restr1.17922034
X-RAY DIFFRACTIONr_sphericity_free2.2922253
X-RAY DIFFRACTIONr_sphericity_bonded1.69822007
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 177
Rwork0.234 3833
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 21.1 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more