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- PDB-9eqb: Iron loaded mitochondrial ferritin H57A/E61A/E64A variant exposed... -

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Basic information

Entry
Database: PDB / ID: 9eqb
TitleIron loaded mitochondrial ferritin H57A/E61A/E64A variant exposed to oxygen for 20 minutes
ComponentsFerritin, mitochondrial
KeywordsMETAL BINDING PROTEIN / Ferritin / mitochondrial / iron / human
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
: / Ferritin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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

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Assembly

Deposited unit
A: Ferritin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,46113
Polymers20,0301
Non-polymers43112
Water4,432246
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)491,070312
Polymers480,72924
Non-polymers10,341288
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area101690 Å2
ΔGint-1985 kcal/mol
Surface area130630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.395, 182.395, 182.395
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-204-

MG

31A-206-

MG

41A-207-

MG

51A-209-

CL

61A-320-

HOH

71A-346-

HOH

81A-509-

HOH

91A-518-

HOH

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Components

#1: Protein Ferritin, mitochondrial


Mass: 20030.389 Da / Num. of mol.: 1 / Mutation: H57A E61A E64A
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
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M bicine 2 M magnesium chloride 100 mM sodium chloride 60 mM ferrous chloride 3 mM sodium azide pH 9.0
PH range: 8.9-9.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.36→54.99 Å / Num. obs: 56043 / % possible obs: 99.97 % / Redundancy: 20 % / Biso Wilson estimate: 15.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 0.58
Reflection shellResolution: 1.36→1.409 Å / Num. unique obs: 5464 / CC1/2: 0.355

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→54.99 Å / SU ML: 0.1714 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.7943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 2809 5.01 %
Rwork0.1745 53221 -
obs0.1758 56030 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.36→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 12 246 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551401
X-RAY DIFFRACTIONf_angle_d0.82181898
X-RAY DIFFRACTIONf_chiral_restr0.0783201
X-RAY DIFFRACTIONf_plane_restr0.0057253
X-RAY DIFFRACTIONf_dihedral_angle_d4.7114188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.36021200.35672604X-RAY DIFFRACTION99.71
1.38-1.410.36511470.32772585X-RAY DIFFRACTION100
1.41-1.440.32471590.29872617X-RAY DIFFRACTION100
1.44-1.470.28691210.24162632X-RAY DIFFRACTION99.96
1.47-1.50.24831370.20192606X-RAY DIFFRACTION99.96
1.5-1.530.21061350.19092639X-RAY DIFFRACTION100
1.53-1.570.2211370.18632612X-RAY DIFFRACTION100
1.57-1.610.20681250.18332635X-RAY DIFFRACTION99.96
1.61-1.660.2361510.18222607X-RAY DIFFRACTION100
1.66-1.710.22811440.1972654X-RAY DIFFRACTION100
1.71-1.770.19861410.18872623X-RAY DIFFRACTION100
1.77-1.850.21381490.16612645X-RAY DIFFRACTION100
1.85-1.930.22411400.15972630X-RAY DIFFRACTION99.96
1.93-2.030.18441370.15352658X-RAY DIFFRACTION100
2.03-2.160.17141360.14732673X-RAY DIFFRACTION100
2.16-2.330.17651470.14952683X-RAY DIFFRACTION100
2.33-2.560.17521440.16242668X-RAY DIFFRACTION100
2.56-2.930.19641370.16532749X-RAY DIFFRACTION100
2.93-3.690.16741400.14792756X-RAY DIFFRACTION100
3.69-54.990.20521620.18472945X-RAY DIFFRACTION99.94

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