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- PDB-7o6a: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -

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Basic information

Entry
Database: PDB / ID: 7o6a
TitleCrystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 5 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


positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport ...positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / 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: 1.4 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)21,89619
Polymers21,1081
Non-polymers78818
Water6,684371
1
A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules

A: Ferritin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,499456
Polymers506,58224
Non-polymers18,918432
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
Unit cell
Length a, b, c (Å)183.675, 183.675, 183.675
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-204-

FE2

31A-206-

FE2

41A-208-

FE2

51A-395-

HOH

61A-498-

HOH

71A-517-

HOH

81A-575-

HOH

91A-614-

HOH

101A-622-

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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.14 Å3/Da / Density % sol: 60.79 % / Description: Octahedral crystals
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 I0410.90001
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
10.900011
21.738921
31.75121
Reflection

Entry-ID: 7O6A / 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)
1.4-106.04525811002214.410.0670.0150.07126.3
2.1-105.921558897.514.716.70.9970.0920.0230.1220.8
2.1-106.021548796.514.820.80.9980.0920.0220.096320.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.4-1.4822.20.9043.775510.8990.20.9441100
2.1-2.212.80.1494.918690.9530.1040.193283.7
2.1-2.212.50.1673.717470.9460.1190.216377.5

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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: 1.4→106.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.374 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1625 2638 5 %RANDOM
Rwork0.1315 ---
obs0.1331 49920 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.41 Å2 / Biso mean: 18.974 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.125 Å
Refinement stepCycle: final / Resolution: 1.4→106.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 421 1841
Biso mean--21.46 28.62 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121640
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6382246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24722.857112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0261513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021315
X-RAY DIFFRACTIONr_rigid_bond_restr2.44631211
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 209 -
Rwork0.188 3612 -
all-3821 -
obs--100 %

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