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- PDB-4bcy: Monomeric Human Cu,Zn Superoxide dismutase, mutation H43F -

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Basic information

Entry
Database: PDB / ID: 4bcy
TitleMonomeric Human Cu,Zn Superoxide dismutase, mutation H43F
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / DISEASE MUTATION BINDING / PROTEIN FOLDING / NEURODEGENERATION / ALS
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / regulation of organ growth / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / regulation of organ growth / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / regulation of GTPase activity / 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 / removal of superoxide radicals / 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 / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / 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 / negative regulation of inflammatory response / small GTPase binding / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / cytoplasmic vesicle / protein-folding chaperone binding / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / positive regulation of apoptotic process / 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
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 (Cu/Zn) / superoxide dismutase copper chaperone / 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
: / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.272 Å
AuthorsAwad, W. / Saraboji, K. / Danielsson, J. / Lang, L. / Kurnik, M. / Marklund, S.L. / Oliveberg, M. / Logan, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Global Structural Motions from the Strain of a Single Hydrogen Bond.
Authors: Danielsson, J. / Awad, W. / Saraboji, K. / Kurnik, M. / Lang, L. / Leinartaite, L. / Marklund, S.L. / Logan, D.T. / Oliveberg, M.
History
DepositionOct 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,76412
Polymers15,8261
Non-polymers93811
Water1,26170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.870, 47.910, 81.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE 1 / HSOD1


Mass: 15826.459 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATIONS C6A, H43F, F50E, G51E, C111A

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 293 K
Details: 25% PEG 400, 0.1M NA ACETATE PH 4.6, 0.1 M CDCL2, 20 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1
DetectorType: MARRESEARCH 165MM / Detector: CCD / Date: Feb 15, 2012 / Details: HORIZONTALLY FOCUSING MIRROR
RadiationMonochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→30 Å / Num. obs: 36511 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.82 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 1.27→1.3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJK

2xjk


Resolution: 1.272→28.193 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 23.27 / Stereochemistry target values: ML
Details: THE REGION AROUND CD IONS 1157 AND 1158, INVOLVED IN A CRYSTAL CONTACT, WAS DIFFICULT TO MODEL UNAMBIGUOUSLY.
RfactorNum. reflection% reflection
Rfree0.2034 1825 5 %
Rwork0.1912 --
obs0.1918 36503 99.87 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.272→28.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 11 70 1149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061130
X-RAY DIFFRACTIONf_angle_d1.0961532
X-RAY DIFFRACTIONf_dihedral_angle_d13.306419
X-RAY DIFFRACTIONf_chiral_restr0.074171
X-RAY DIFFRACTIONf_plane_restr0.004207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2715-1.30590.3061310.30162631X-RAY DIFFRACTION100
1.3059-1.34430.30831320.2772645X-RAY DIFFRACTION100
1.3443-1.38770.29641410.24582607X-RAY DIFFRACTION100
1.3877-1.43730.27961330.23422628X-RAY DIFFRACTION100
1.4373-1.49490.20641440.21432640X-RAY DIFFRACTION100
1.4949-1.56290.22531240.20382647X-RAY DIFFRACTION100
1.5629-1.64530.22091430.19552663X-RAY DIFFRACTION100
1.6453-1.74840.20611520.18882625X-RAY DIFFRACTION100
1.7484-1.88330.20931230.19222665X-RAY DIFFRACTION100
1.8833-2.07280.18351370.1932688X-RAY DIFFRACTION100
2.0728-2.37260.20181500.19092681X-RAY DIFFRACTION100
2.3726-2.98870.23971650.20242701X-RAY DIFFRACTION100
2.9887-28.20020.17631500.17492857X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.7713 Å / Origin y: -3.6712 Å / Origin z: -10.2773 Å
111213212223313233
T0.138 Å2-0.0084 Å20.0028 Å2-0.1319 Å20.0115 Å2--0.1263 Å2
L1.6765 °20.2858 °2-0.816 °2-2.4544 °2-1.0745 °2--3.3369 °2
S0.013 Å °0.0632 Å °0.1345 Å °-0.107 Å °0.1362 Å °0.1228 Å °-0.0758 Å °-0.2128 Å °-0.1133 Å °
Refinement TLS groupSelection details: ALL

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