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- PDB-9eq9: Iron loaded mitochondrial ferritin, anaerobic -

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Basic information

Entry
Database: PDB / ID: 9eq9
TitleIron loaded mitochondrial ferritin, anaerobic
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: 1.84 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)20,96423
Polymers20,2141
Non-polymers75022
Water1,49583
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)503,126552
Polymers485,12524
Non-polymers18,001528
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 area85600 Å2
ΔGint-1102 kcal/mol
Surface area135960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.430, 177.430, 177.430
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-204-

FE

21A-205-

MG

31A-206-

MG

41A-207-

MG

51A-210-

MG

61A-214-

MG

71A-215-

CL

81A-216-

CL

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Components

#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
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting 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: 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: 1.84→51.22 Å / Num. obs: 21331 / % possible obs: 89.8 % / Redundancy: 21.3 % / Biso Wilson estimate: 34.81 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.64
Reflection shellResolution: 1.841→1.906 Å / Num. unique obs: 2088 / CC1/2: 0.364 / CC star: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→51.22 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 1080 5.06 %
Rwork0.2043 20246 -
obs0.2064 21326 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.79 Å2
Refinement stepCycle: LAST / Resolution: 1.84→51.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 22 83 1454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01261397
X-RAY DIFFRACTIONf_angle_d1.24471890
X-RAY DIFFRACTIONf_chiral_restr0.0636199
X-RAY DIFFRACTIONf_plane_restr0.01251
X-RAY DIFFRACTIONf_dihedral_angle_d5.2829185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.920.37831460.31592444X-RAY DIFFRACTION99.92
1.92-2.030.34951130.28512496X-RAY DIFFRACTION100
2.03-2.150.28151350.23312479X-RAY DIFFRACTION100
2.15-2.320.25511330.21022489X-RAY DIFFRACTION100
2.32-2.550.27511470.22582491X-RAY DIFFRACTION100
2.55-2.920.25691510.22432511X-RAY DIFFRACTION100
2.92-3.680.25771360.18442567X-RAY DIFFRACTION100
3.68-51.220.20011190.18492769X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.093033565981.724050600492.569561489293.15932254044.24036789046.92332011347-0.07968584721180.462541765774-0.111901590759-0.4853261914060.09528368793660.1641856404040.06763428293430.146621837352-0.0529042487470.2785166823240.0128089948074-0.001328714311690.2525008191410.01100757040070.249541830351-50.5038739377-35.6385416997-8.89799801167
24.779387988147.053669618196.478652977965.391933409356.683414456245.267883575740.118527830418-0.3631129642020.35218180037-0.0939303351314-0.4642260409750.367562552343-0.104625364445-0.441005447430.383455465710.3093204676030.01233206474640.002236070896710.306938588753-0.02890894148430.349837989618-53.4274074486-26.2443222332-3.84744033369
37.929854594740.1977056193884.219192804761.952476043672.588058897155.407450225611.00525505687-0.164359206527-1.4015519713-1.220199216440.07209858769420.01843614193630.459295808358-0.730862606257-0.7135209149720.5129240337930.00605878983239-0.05253521186470.2832555990590.005811090676560.44948779614-62.4648659489-45.9188648518-15.3102657793
45.721163553497.815056832783.284767420839.836051043723.962099940331.643027257780.236577033749-0.0602939908135-0.748650254487-0.0213237218652-0.0837606175858-1.19342041902-0.0525436539195-0.000335787329678-0.1932825066060.3631291194190.01523580523410.01715022237770.294642164427-0.03536669681090.369634707261-42.7587158286-33.9803890576-1.3028131966
56.956315132583.946127656966.221815102613.852286432865.288400089417.253250755750.0569531301240.287858811716-0.3046092912030.1295895971960.286744581316-0.2599542937940.2558333864240.433270607773-0.3626292442460.268363318277-0.0002624806364750.03446554828590.2670557368440.01827824801570.243185582624-44.6587659491-29.7622970075-15.8924124373
66.887545074486.247087967574.494349391257.855626330986.056039457774.77598295038-0.116905687174-0.007805854885570.105106835839-0.252614421641-0.1211155539730.512193079293-0.278445862109-0.06132847677610.3213517679720.3684101735380.0371338863767-0.002027542702110.3070588047760.007622225226160.332436920671-58.6323018159-34.3787179825-23.3517786073
70.8827584935353.211970002532.050978499618.987050206316.078717198853.72933931359-0.1072154599490.05677834922780.147169091777-0.353018555854-0.0319275783118-0.104013568015-0.2825219390560.06360432792120.07607669096220.2692903541160.00447891971094-0.009136647481470.2846817260810.02587590784210.282921357061-43.0697080394-13.5586172868-7.90617381285
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 41 )11 - 411 - 31
22chain 'A' and (resid 42 through 75 )42 - 7532 - 65
33chain 'A' and (resid 76 through 80 )76 - 8066 - 70
44chain 'A' and (resid 81 through 95 )81 - 9571 - 85
55chain 'A' and (resid 96 through 123 )96 - 12386 - 113
66chain 'A' and (resid 124 through 137 )124 - 137114 - 127
77chain 'A' and (resid 138 through 176 )138 - 176128 - 166

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