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- PDB-7o6c: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -

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Basic information

Entry
Database: PDB / ID: 7o6c
TitleCrystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 15 minutes under anaerobic environment
ComponentsFerritin, mitochondrial
KeywordsOXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / anaerobic environment
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / protein maturation / iron ion transport / Iron uptake and transport / ferrous iron binding / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding ...ferroxidase / ferroxidase activity / ferric iron binding / protein maturation / iron ion transport / Iron uptake and transport / ferrous iron binding / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like ...Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPozzi, C. / Ciambellotti, S. / Tassone, G. / Turano, P. / Mangani, S.
CitationJournal: Chemistry / Year: 2021
Title: Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin.
Authors: Ciambellotti, S. / Pratesi, A. / Tassone, G. / Turano, P. / Mangani, S. / Pozzi, C.
History
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)22,09026
Polymers21,1081
Non-polymers98325
Water6,630368
1
A: Ferritin, mitochondrial
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)530,163624
Polymers506,58224
Non-polymers23,582600
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation31_554-z,-x+1/2,y-1/21
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation82_555-y+1/2,z+1/2,-x1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation83_455y-1/2,-z+1/2,-x1
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation81_455y-1/2,z+1/2,x1
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation32_555-z,x+1/2,-y+1/21
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
crystal symmetry operation24_565-z,-y+1,-x1
crystal symmetry operation29_554z,x+1/2,y-1/21
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
Buried area90606 Å2
ΔGint-332.7 kcal/mol
Surface area139372 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.449, 182.449, 182.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

FE2

21A-206-

FE2

31A-207-

FE2

41A-212-

MG

51A-325-

HOH

61A-329-

HOH

71A-497-

HOH

81A-511-

HOH

91A-558-

HOH

101A-602-

HOH

111A-611-

HOH

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Components

#1: Protein Ferritin, mitochondrial


Mass: 21107.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTMT / Plasmid: pET-3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: Q8N4E7, ferroxidase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.87
SYNCHROTRONDiamond I0421.73892
SYNCHROTRONDiamond I0431.7512
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELMay 17, 2019
DECTRIS PILATUS 6M-F2PIXELMay 17, 2019
DECTRIS PILATUS 6M-F3PIXELMay 17, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)MADMx-ray2
3Si(111)MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.738921
31.75121
Reflection

Entry-ID: 7O6C / Observed criterion σ(I): 2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.2-55.018110310020.19.910.0660.0150.07122
2.2-55.041356798.516.311.70.9980.0720.0190.083225.3
2.2-55.081354398.216.2100.9990.0440.0110.048344
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.2-1.2614.10.763.3116650.8690.2150.8171100
2.2-2.325.50.1157.117490.9840.0560.139291.1
2.2-2.325.10.0571517170.9950.0290.068389.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R03

1r03


Resolution: 1.2→52.72 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.775 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1425 4101 5.1 %RANDOM
Rwork0.1212 ---
obs0.1222 76990 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.2 Å2 / Biso mean: 13.691 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.114 Å
Refinement stepCycle: final / Resolution: 1.2→52.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 25 423 1851
Biso mean--18.07 25.32 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171551
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6452334
X-RAY DIFFRACTIONr_angle_other_deg1.5911.5863621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3523.333114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11915313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3581512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
X-RAY DIFFRACTIONr_rigid_bond_restr1.68431130
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 278 -
Rwork0.188 5624 -
all-5902 -
obs--99.9 %

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