[English] 日本語
Yorodumi
- PDB-3gqf: Structural and Biophysical Properties of the Pathogenic SOD1 Vari... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gqf
TitleStructural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU-ZN SUPEROXIDE DISMUTASE / SUPEROXIDE ACCEPTOR / FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS MUTANT / Acetylation / Amyotrophic lateral sclerosis / Antioxidant / Copper / Cytoplasm / Disease mutation / Disulfide bond / Metal-binding / Phosphoprotein / Ubl conjugation / Zinc
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / 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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / 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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / : / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / positive regulation of superoxide anion generation / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / placenta development / locomotory behavior / determination of adult lifespan / sensory perception of sound / regulation of blood pressure / negative regulation of inflammatory response / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / Platelet degranulation / peroxisome / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWinkler, D.D. / Schuermann, J.P. / Hart, P.J.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and biophysical properties of the pathogenic SOD1 variant H46R/H48Q.
Authors: Winkler, D.D. / Schuermann, J.P. / Cao, X. / Holloway, S.P. / Borchelt, D.R. / Carroll, M.C. / Proescher, J.B. / Culotta, V.C. / Hart, P.J.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,61217
Polymers95,0206
Non-polymers59311
Water8,971498
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8846
Polymers31,6732
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-35 kcal/mol
Surface area14070 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8846
Polymers31,6732
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-33 kcal/mol
Surface area13930 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8445
Polymers31,6732
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-23 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.576, 194.331, 143.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11F-424-

HOH

DetailsDIMER

-
Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15836.590 Da / Num. of mol.: 6 / Mutation: H46R, H48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.15 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 5, 2007 / Details: mirrors
RadiationMonochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 79657 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7908 / Rsym value: 0.503 / % possible all: 100

-
Processing

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

1azv


Resolution: 2.2→28.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24229 3992 5 %RANDOM
Rwork0.20512 ---
obs0.20699 75634 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 11 498 7169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9529116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.63225.625288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.127151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5021530
X-RAY DIFFRACTIONr_chiral_restr0.090.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025154
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.22852
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24519
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2520
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.54470
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44127104
X-RAY DIFFRACTIONr_scbond_it2.0632290
X-RAY DIFFRACTIONr_scangle_it3.4154.52012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 289 -
Rwork0.245 5502 -
obs-5502 99.64 %

+
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://pdbjlvh1.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