[English] 日本語
Yorodumi
- PDB-8iq1: Crystal structure of hydrogen sulfide-bound superoxide dismutase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iq1
TitleCrystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / dimer
Function / homology
Function and homology information


neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / 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 / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / : / locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 (II) ION / HYDROSULFURIC ACID / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhou, J.H. / Huang, W.X. / Cheng, R.X. / Zhang, P.J. / Zhu, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071446 China
CitationJournal: Cell Rep / Year: 2023
Title: Hydrogen sulfide functions as a micro-modulator bound at the copper active site of Cu/Zn-SOD to regulate the catalytic activity of the enzyme.
Authors: Wu, D.D. / Jin, S. / Cheng, R.X. / Cai, W.J. / Xue, W.L. / Zhang, Q.Q. / Yang, L.J. / Zhu, Q. / Li, M.Y. / Lin, G. / Wang, Y.Z. / Mu, X.P. / Wang, Y. / Zhang, I.Y. / Zhang, Q. / Chen, Y. / ...Authors: Wu, D.D. / Jin, S. / Cheng, R.X. / Cai, W.J. / Xue, W.L. / Zhang, Q.Q. / Yang, L.J. / Zhu, Q. / Li, M.Y. / Lin, G. / Wang, Y.Z. / Mu, X.P. / Wang, Y. / Zhang, I.Y. / Zhang, Q. / Chen, Y. / Cai, S.Y. / Tan, B. / Li, Y. / Chen, Y.Q. / Zhang, P.J. / Sun, C. / Yin, Y. / Wang, M.J. / Zhu, Y.Z. / Tao, B.B. / Zhou, J.H. / Huang, W.X. / Zhu, Y.C.
History
DepositionMar 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

-
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]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,37055
Polymers124,5878
Non-polymers2,78347
Water20,8791159
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,88114
Polymers31,1472
Non-polymers73412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82013
Polymers31,1472
Non-polymers67311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,85014
Polymers31,1472
Non-polymers70312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82014
Polymers31,1472
Non-polymers67312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.126, 69.961, 91.345
Angle α, β, γ (deg.)98.690, 94.830, 103.310
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 8 or (resid 9...
d_2ens_1(chain "B" and (resid 1 through 2 or (resid 3...
d_3ens_1(chain "C" and (resid 1 through 8 or (resid 9...
d_4ens_1(chain "D" and (resid 1 through 2 or (resid 3...
d_5ens_1(chain "E" and (resid 1 through 8 or (resid 9...
d_6ens_1(chain "F" and (resid 1 through 2 or (resid 3...
d_7ens_1(chain "G" and (resid 1 through 8 or (resid 9...
d_8ens_1(chain "H" and (resid 1 through 2 or (resid 3...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLYGLYAA1 - 541 - 54
d_12THRTHRGLYGLYAA56 - 12556 - 125
d_13ASNASNALAALAAA129 - 143129 - 143
d_14GLYGLYLYSLYSAA145 - 151145 - 151
d_21ALAALAGLYGLYBB1 - 541 - 54
d_22THRTHRGLYGLYBB56 - 12556 - 125
d_23ASNASNALAALABB129 - 143129 - 143
d_24GLYGLYLYSLYSBB145 - 151145 - 151
d_31ALAALAGLYGLYCC1 - 541 - 54
d_32THRTHRGLYGLYCC56 - 12556 - 125
d_33ASNASNALAALACC129 - 143129 - 143
d_34GLYGLYLYSLYSCC145 - 151145 - 151
d_41ALAALAGLYGLYDD1 - 541 - 54
d_42THRTHRGLYGLYDD56 - 12556 - 125
d_43ASNASNALAALADD129 - 143129 - 143
d_44GLYGLYLYSLYSDD145 - 151145 - 151
d_51ALAALAGLYGLYEE1 - 541 - 54
d_52THRTHRGLYGLYEE56 - 12556 - 125
d_53ASNASNALAALAEE129 - 143129 - 143
d_54GLYGLYLYSLYSEE145 - 151145 - 151
d_61ALAALAGLYGLYFF1 - 541 - 54
d_62THRTHRGLYGLYFF56 - 12556 - 125
d_63ASNASNALAALAFF129 - 143129 - 143
d_64GLYGLYLYSLYSFF145 - 151145 - 151
d_71ALAALAGLYGLYGG1 - 541 - 54
d_72THRTHRALAALAGG56 - 14356 - 143
d_73GLYGLYLYSLYSGG145 - 151145 - 151
d_81ALAALAGLYGLYHH1 - 541 - 54
d_82THRTHRGLYGLYHH56 - 12556 - 125
d_83ASNASNALAALAHH129 - 143129 - 143
d_84GLYGLYLYSLYSHH145 - 151145 - 151

NCS oper:
IDCodeMatrixVector
1given(-0.60409619363, -0.770004079093, 0.205332674025), (-0.76049570021, 0.48002772582, -0.437286716475), (0.238147178871, -0.420317856656, -0.875567713299)-31.7621586709, -3.71080819699, 43.6861754587
2given(0.854253805419, 0.453710878328, 0.253765393257), (0.445857213429, -0.890450552042, 0.0911545917751), (0.267323364413, 0.0352739741971, -0.962961040532)16.8520729723, -84.8555736785, 24.2183625294
3given(-0.797911564199, -0.554197701693, -0.23706970105), (0.434639388828, -0.801482579173, 0.41074843513), (-0.417643074165, 0.224701096393, 0.880388368779)-1.3029752451, -91.7652828371, -26.1036493117
4given(0.751910548339, 0.657666809667, -0.0458791320538), (0.513252743109, -0.540283398549, 0.666832415936), (0.413765814183, -0.524945917895, -0.743794080575)25.3366406798, -100.518588281, 45.288103812
5given(-0.972804371029, -0.218909191014, -0.0756995495194), (0.231379196716, -0.933549431063, -0.273768382193), (-0.0107388563146, -0.283838379806, 0.95881199988)-2.65790274613, -84.5060376702, 1.13967548827
6given(-0.757986107878, -0.65129687324, 0.0356292460162), (-0.621327237876, 0.737574197406, 0.264455604581), (-0.198518320909, 0.178316253408, -0.963739482451)-22.0554414257, -8.84856624829, 18.7211306606
7given(0.973612566339, 0.213836749442, 0.0797020404678), (-0.108852299449, 0.74211968562, -0.661369449794), (-0.200573546539, 0.635241856936, 0.74581367353)5.23432312795, 19.8341521472, -18.5037477747

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15573.337 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00442, superoxide dismutase

-
Non-polymers , 8 types, 1206 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 100956 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.98 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.05 / Net I/σ(I): 99.5
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.546 / Num. unique obs: 4846 / CC1/2: 0.783

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.28 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.7476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 4588 4.99 %
Rwork0.1836 87435 -
obs0.1853 92023 90.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8586 0 114 1159 9859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828838
X-RAY DIFFRACTIONf_angle_d1.012111951
X-RAY DIFFRACTIONf_chiral_restr0.06751365
X-RAY DIFFRACTIONf_plane_restr0.00721605
X-RAY DIFFRACTIONf_dihedral_angle_d13.1593092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.429074338723
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.303801948722
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.471865211005
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.39304570536
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.44128673872
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.446405347384
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.416235424425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.308980.27791831X-RAY DIFFRACTION57.43
1.82-1.840.3176990.26092237X-RAY DIFFRACTION68.67
1.84-1.860.27171230.24392358X-RAY DIFFRACTION73.53
1.86-1.890.3021250.23422478X-RAY DIFFRACTION78.22
1.89-1.910.27181570.22862717X-RAY DIFFRACTION84.18
1.91-1.940.24751570.22682825X-RAY DIFFRACTION88.57
1.94-1.970.26951500.22352955X-RAY DIFFRACTION92.63
1.97-20.251570.22083010X-RAY DIFFRACTION93.67
2-2.030.27421570.22442966X-RAY DIFFRACTION93.59
2.03-2.060.24731660.21682938X-RAY DIFFRACTION90.63
2.06-2.090.27031620.21193029X-RAY DIFFRACTION94.19
2.09-2.130.25081670.20963076X-RAY DIFFRACTION96.83
2.13-2.170.2251680.20223106X-RAY DIFFRACTION97.09
2.17-2.220.21971620.20693100X-RAY DIFFRACTION96.85
2.22-2.270.24221660.19993102X-RAY DIFFRACTION97.03
2.27-2.320.26241480.20283128X-RAY DIFFRACTION96.47
2.32-2.380.24551730.1973049X-RAY DIFFRACTION96.44
2.38-2.440.25031760.20533018X-RAY DIFFRACTION94.69
2.44-2.510.23471440.19772889X-RAY DIFFRACTION90.24
2.51-2.590.25171580.20433171X-RAY DIFFRACTION97.34
2.59-2.690.2281740.20423113X-RAY DIFFRACTION97.51
2.69-2.790.23531520.19583095X-RAY DIFFRACTION96.72
2.79-2.920.23491570.20013111X-RAY DIFFRACTION96.8
2.92-3.080.2261790.1913047X-RAY DIFFRACTION95.39
3.08-3.270.21911520.17942845X-RAY DIFFRACTION89.12
3.27-3.520.17381500.16343156X-RAY DIFFRACTION97.26
3.52-3.870.19161490.15233111X-RAY DIFFRACTION97.23
3.88-4.430.17671650.13393030X-RAY DIFFRACTION94.95
4.44-5.580.14231410.1282968X-RAY DIFFRACTION92.42
5.59-38.280.14621560.14962976X-RAY DIFFRACTION92.72

+
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