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- PDB-9eq8: Iron loaded mitochondrial ferritin exposed to oxygen for 2 minutes -

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Basic information

Entry
Database: PDB / ID: 9eq8
TitleIron loaded mitochondrial ferritin exposed to oxygen for 2 minutes
ComponentsFerritin, mitochondrial
KeywordsMETAL BINDING PROTEIN / Ferritin / mitochondrial / iron
Function / homology
Function and homology information


positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / ferroxidase / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis ...positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / : / ferroxidase / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding / positive regulation of cell population proliferation / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / HYDROGEN PEROXIDE / Ferritin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBugg, Z. / Bradley, J.M. / Le Brun, N.E. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002363/1 United Kingdom
CitationJournal: To Be Published
Title: The core nucleation site of human mitochondrial ferritin: observation of the nascent mineral
Authors: Bradley, J.M. / Bugg, Z. / Moore, G.R. / Hemmings, A.M. / Le-Brun, N.
History
DepositionMar 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,99824
Polymers20,2141
Non-polymers78423
Water3,315184
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)503,942576
Polymers485,12524
Non-polymers18,818552
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_455-x-1,z,y1
crystal symmetry operation19_455-x-1,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_454-y-1/2,z,-x-1/21
crystal symmetry operation59_454y-1/2,-z,-x-1/21
crystal symmetry operation60_455-y-1/2,-z,x+1/21
crystal symmetry operation69_454z-1/2,y,-x-1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_455-z-1/2,y,x+1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_445z-1/2,-x-1/2,-y1
crystal symmetry operation79_445-z-1/2,-x-1/2,y1
crystal symmetry operation80_455-z-1/2,x+1/2,-y1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_445y-1/2,-x-1/2,z1
crystal symmetry operation88_455-y-1/2,x+1/2,z1
Buried area93860 Å2
ΔGint-1200 kcal/mol
Surface area140750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.770, 182.770, 182.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x,y+1/2,z+1/2
#26: x,-z+1/2,y+1/2
#27: x,z+1/2,-y+1/2
#28: z,y+1/2,-x+1/2
#29: -z,y+1/2,x+1/2
#30: -y,x+1/2,z+1/2
#31: y,-x+1/2,z+1/2
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y,x+1/2,-z+1/2
#44: -y,-x+1/2,-z+1/2
#45: z,-y+1/2,x+1/2
#46: -z,-y+1/2,-x+1/2
#47: -x,z+1/2,y+1/2
#48: -x,-z+1/2,-y+1/2
#49: x+1/2,y,z+1/2
#50: x+1/2,-z,y+1/2
#51: x+1/2,z,-y+1/2
#52: z+1/2,y,-x+1/2
#53: -z+1/2,y,x+1/2
#54: -y+1/2,x,z+1/2
#55: y+1/2,-x,z+1/2
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+1/2,x,-z+1/2
#68: -y+1/2,-x,-z+1/2
#69: z+1/2,-y,x+1/2
#70: -z+1/2,-y,-x+1/2
#71: -x+1/2,z,y+1/2
#72: -x+1/2,-z,-y+1/2
#73: x+1/2,y+1/2,z
#74: x+1/2,-z+1/2,y
#75: x+1/2,z+1/2,-y
#76: z+1/2,y+1/2,-x
#77: -z+1/2,y+1/2,x
#78: -y+1/2,x+1/2,z
#79: y+1/2,-x+1/2,z
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+1/2,x+1/2,-z
#92: -y+1/2,-x+1/2,-z
#93: z+1/2,-y+1/2,x
#94: -z+1/2,-y+1/2,-x
#95: -x+1/2,z+1/2,y
#96: -x+1/2,-z+1/2,-y
Components on special symmetry positions
IDModelComponents
11A-203-

FE

21A-205-

MG

31A-206-

MG

41A-207-

MG

51A-221-

CL

61A-222-

CL

71A-323-

HOH

81A-480-

HOH

91A-481-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin, mitochondrial


Mass: 20213.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N4E7, ferroxidase

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Non-polymers , 5 types, 207 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M bicine 2.0 M magnesium chloride 100 mM sodium chloride 60 mM ferrous chloride 3 mM sodium azide pH 9.0
PH range: 8.9-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.48→40.87 Å / Num. obs: 43961 / % possible obs: 99.91 % / Redundancy: 16.83 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 1.17
Reflection shellResolution: 1.48→1.533 Å / Num. unique obs: 4285 / CC1/2: 0.391

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→40.87 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.182 2107 4.79 %
Rwork0.1652 41848 -
obs0.1661 43955 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.03 Å2
Refinement stepCycle: LAST / Resolution: 1.48→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 24 184 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821412
X-RAY DIFFRACTIONf_angle_d1.10681909
X-RAY DIFFRACTIONf_chiral_restr0.0867201
X-RAY DIFFRACTIONf_plane_restr0.0075254
X-RAY DIFFRACTIONf_dihedral_angle_d4.928187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.33321470.28912711X-RAY DIFFRACTION99.2
1.51-1.550.27241150.26862712X-RAY DIFFRACTION99.93
1.55-1.590.28351390.22862734X-RAY DIFFRACTION99.97
1.59-1.640.26081450.20452759X-RAY DIFFRACTION100
1.64-1.690.21271330.1732741X-RAY DIFFRACTION100
1.69-1.750.19711430.1542761X-RAY DIFFRACTION100
1.76-1.820.17481120.14232765X-RAY DIFFRACTION100
1.83-1.910.17671510.14072764X-RAY DIFFRACTION100
1.91-2.010.18091590.13992747X-RAY DIFFRACTION100
2.01-2.130.15471340.13192792X-RAY DIFFRACTION100
2.14-2.30.15611360.1372784X-RAY DIFFRACTION99.97
2.3-2.530.16661400.14562817X-RAY DIFFRACTION99.97
2.53-2.90.18641540.16022810X-RAY DIFFRACTION99.97
2.9-3.650.14821370.15532880X-RAY DIFFRACTION100
3.65-40.870.18771620.18393071X-RAY DIFFRACTION99.91

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