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- PDB-9eqa: Iron loaded mitochondrial ferritin exposed to oxygen for 20 minutes -

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Basic information

Entry
Database: PDB / ID: 9eqa
TitleIron loaded mitochondrial ferritin 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: 1.97 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)20,90516
Polymers20,2141
Non-polymers69115
Water1,38777
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)501,712384
Polymers485,12524
Non-polymers16,587360
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 area81430 Å2
ΔGint-696 kcal/mol
Surface area138910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.526, 182.526, 182.526
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-210-

FE

21A-211-

MG

31A-212-

MG

41A-213-

MG

51A-214-

MG

61A-215-

CL

71A-310-

HOH

81A-354-

HOH

91A-374-

HOH

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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.: 10 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2 M magnesium chloride 100 mM sodium chloride 3 mM sodium azide 100 mM bicine 60 mM ferrous chloride 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: 1.97→105.38 Å / Num. obs: 32993 / % possible obs: 94.8 % / Redundancy: 20 % / Biso Wilson estimate: 40.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1513 / Rpim(I) all: 0.0261 / Rrim(I) all: 0.1536 / Net I/σ(I): 11.82
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1862 / CC1/2: 0.462 / CC star: 0.795 / Rpim(I) all: 0.6811 / % possible all: 59

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→105.38 Å / SU ML: 0.3276 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 1695 5.14 %
Rwork0.1878 31298 -
obs0.1903 32993 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.19 Å2
Refinement stepCycle: LAST / Resolution: 1.97→105.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 15 77 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121394
X-RAY DIFFRACTIONf_angle_d1.24051886
X-RAY DIFFRACTIONf_chiral_restr0.0515199
X-RAY DIFFRACTIONf_plane_restr0.0113250
X-RAY DIFFRACTIONf_dihedral_angle_d5.5326186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.4264760.38581115X-RAY DIFFRACTION41.21
2.03-2.090.38461390.32182676X-RAY DIFFRACTION96.08
2.09-2.170.30421250.27352751X-RAY DIFFRACTION100
2.17-2.250.26491340.24612781X-RAY DIFFRACTION100
2.26-2.360.30541380.25192750X-RAY DIFFRACTION99.97
2.36-2.480.25991640.20752747X-RAY DIFFRACTION100
2.48-2.640.26631380.21152724X-RAY DIFFRACTION100
2.64-2.840.25681450.19972775X-RAY DIFFRACTION99.97
2.84-3.130.27391820.19242709X-RAY DIFFRACTION100
3.13-3.580.20261310.15242782X-RAY DIFFRACTION100
3.58-4.510.17331710.13382715X-RAY DIFFRACTION100
4.51-105.380.22171520.18922773X-RAY DIFFRACTION99.76
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)
10.0404028813109-0.150598527527-0.07143532730880.420983331945-0.2807881341040.2820096992170.01359401748270.0347192643638-0.0464718587788-0.03073588957970.0591513007135-0.1358093199140.002629475048290.167438672036-0.0001805277763670.3304373346820.009599538680710.007254861054090.336701014973-0.01685284792180.321787278354-51.3688994973-32.7814075837-5.84861815697
20.5503111447070.224364787441-0.4196374135530.230090243579-0.2689830314550.192759484517-0.0510916359968-0.03214300730370.290108098436-0.0568452022784-0.07846339973340.348141659885-0.0274580777039-0.1369170412390.0001680981908890.2132618728750.0350590598736-0.02214191300610.2262074422190.01408023960.225650837488-58.6246358699-28.6390341253-7.23868508298
30.00709510557091-0.008671607707120.01113543930340.009673248126430.0119923740354-0.0112885830483-0.151193407721-0.10815303065-0.1130646370990.416300076668-0.123974987369-0.2849794990460.05343868734250.1877189268951.38223030443E-60.471890576221-0.0202237265959-0.01517873489790.358009635442-0.05030141208380.457462478349-62.1115812873-47.695004129-12.2937973396
4-0.06426202062480.03543180040670.1704895023480.0805728851023-0.2720241928590.07428234130410.335821433927-0.204632412433-0.3569235997050.357338149775-0.324637965849-0.4826959054430.0923832492703-0.01464679926010.0002324549013430.407037764484-0.0212221238894-0.02232703555260.3512128320520.02103691552080.355020717893-44.2700560198-33.3161527641-0.701191110387
50.3043508739230.116022984806-0.04267905566640.1729723322620.335985343399-0.0046276126132-0.001152378182640.02267010975-0.0451624597978-0.0508713587490.03815804975560.0137018590416-0.09695273222780.03398260879051.83568324784E-50.383526441095-0.00778176209123-0.002983873520140.37972231925-0.006366028159730.358692066474-52.0793117785-31.5263221061-18.6975950276
60.0383973570421-0.0906090060921-0.05979446920510.362774169565-0.05335247686560.121152355759-0.01571301596660.06509516348710.0858455517878-0.183719007189-0.0373810175336-0.001792690313910.01558738839760.08129814432553.57888946695E-50.1805266325270.0009893113355360.01520110560820.148062696888-0.003900316734170.149852077516-45.6251265489-13.5689348339-7.95287254386
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 48 )11 - 481 - 38
22chain 'A' and (resid 49 through 76 )49 - 7639 - 66
33chain 'A' and (resid 77 through 81 )77 - 8167 - 71
44chain 'A' and (resid 82 through 95 )82 - 9572 - 85
55chain 'A' and (resid 96 through 137 )96 - 13786 - 127
66chain 'A' and (resid 138 through 176 )138 - 176128 - 166

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