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- PDB-6fon: Elongated conformer of the human copper chaperone for SOD1 comple... -

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Basic information

Entry
Database: PDB / ID: 6fon
TitleElongated conformer of the human copper chaperone for SOD1 complexed with human SOD1
Components
  • Copper chaperone for superoxide dismutase
  • Superoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / chaperone / zinc / copper / heterodimer
Function / homology
Function and homology information


protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / 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 ...protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / 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 / 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 / protein-disulfide reductase activity / 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 / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / 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 / cellular response to oxidative stress / gene expression / response to heat / protein-folding chaperone binding / 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 / cadherin binding / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / 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
Similarity search - Domain/homology
Copper chaperone for superoxide dismutase / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWright, G.S.A. / Sala, F.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
Funding support United Kingdom, Brazil, 6items
OrganizationGrant numberCountry
Motor Neurone Disease AssociationHasnain/Apr15/833-791 United Kingdom
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA United Kingdom
Sao Paulo Research Fundation2015/00062-1 Brazil
Sao Paulo Research Fundation2016/24686-7 Brazil
National Council for Scientific and Technological Development407438/2013-0 Brazil
National Council for Scientific and Technological Development (CNPq)407438/2013-0 Brazil
CitationJournal: Plos Biol. / Year: 2019
Title: Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS.
Authors: Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper chaperone for superoxide dismutase
B: Superoxide dismutase [Cu-Zn]
C: Copper chaperone for superoxide dismutase
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4818
Polymers85,2194
Non-polymers2624
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-21 kcal/mol
Surface area40490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.481, 172.481, 219.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILEAA8 - 2591 - 252
21GLNGLNILEILECC8 - 2591 - 252
12ALAALAGLNGLNBB1 - 1531 - 153
22ALAALAGLNGLNDD1 - 1531 - 153

NCS ensembles :
ID
1
2

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Components

#1: Protein Copper chaperone for superoxide dismutase / Superoxide dismutase copper chaperone


Mass: 26846.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCS / Production host: Escherichia coli (E. coli) / References: UniProt: O14618
#2: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15763.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0 0.2 M Magnesium chloride 20 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.05→44.19 Å / Num. obs: 24090 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.036 / Rrim(I) all: 0.135 / Net I/σ(I): 18.7
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.429 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3485 / CC1/2: 0.693 / Rpim(I) all: 0.384 / Rrim(I) all: 1.481 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOL

6fol


Resolution: 3.05→44.19 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.905 / SU B: 20.088 / SU ML: 0.332 / Cross valid method: FREE R-VALUE / ESU R Free: 0.391
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS WAS USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24628 1234 5.1 %RANDOM
Rwork0.19867 ---
obs0.20134 22855 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----3.21 Å2
Refinement stepCycle: 1 / Resolution: 3.05→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 4 2 5935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196065
X-RAY DIFFRACTIONr_bond_other_d0.0020.025506
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9518210
X-RAY DIFFRACTIONr_angle_other_deg0.945312800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1855814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72725276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16115981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8171538
X-RAY DIFFRACTIONr_chiral_restr0.0790.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021143
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4179.3963256
X-RAY DIFFRACTIONr_mcbond_other6.4149.3953255
X-RAY DIFFRACTIONr_mcangle_it9.81914.0874070
X-RAY DIFFRACTIONr_mcangle_other9.81814.0884071
X-RAY DIFFRACTIONr_scbond_it5.9699.62809
X-RAY DIFFRACTIONr_scbond_other5.979.62806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.25814.284139
X-RAY DIFFRACTIONr_long_range_B_refined12.9276171
X-RAY DIFFRACTIONr_long_range_B_other12.9266172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137360.1
12C137360.1
21B88700.09
22D88700.09
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 60 -
Rwork0.371 1688 -
obs--100 %

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