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- PDB-1r03: crystal structure of a human mitochondrial ferritin -

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Basic information

Entry
Database: PDB / ID: 1r03
Titlecrystal structure of a human mitochondrial ferritin
Componentsmitochondrial ferritin
KeywordsMETAL BINDING PROTEIN / iron storage / ferritin / x-ray crystallography
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, 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: 1.7 Å
AuthorsCorsi, B. / Santambrogio, P. / Arosio, P. / Levi, S. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B. / Chevallier, J.M. / Precigoux, G.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure and Biochemical Properties of the Human Mitochondrial Ferritin and its Mutant Ser144Ala
Authors: Langlois d'Estaintot, B. / Santambrogio, P. / Granier, T. / Gallois, B. / Chevallier, J.M. / Precigoux, G. / Levi, S. / Arosio, P.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: A human mitochondrial ferritin encoded by an intronless gene
Authors: Levi, S. / Corsi, B. / Bosisio, M. / Invernizzi, R. / Volz, A. / Sanford, D. / Arosio, P. / Drysdale, J.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution ferritins at high resolution
Authors: Hempstead, P.D. / Yewdall, S.J. / Alistair, R. / Lawson, D.M. / Artymiuk, P.J. / Rice, D.W. / Ford, G.C. / Harrison, P.M.
History
DepositionSep 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mitochondrial ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0986
Polymers20,9761
Non-polymers1225
Water3,783210
1
A: mitochondrial ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)506,349144
Polymers503,43324
Non-polymers2,917120
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 area99520 Å2
ΔGint-1077 kcal/mol
Surface area129000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.410, 181.410, 181.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Cell settingcubic
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-306-

MG

31A-516-

HOH

41A-579-

HOH

51A-638-

HOH

Detailscoordinates for a complete multimer representing the known biologically significant oligomerization state of the molecule can be generated by applying the the symmetry operations: -x,-y,z; -x,y,-z; x,-y,-z; z,x,y; z,-x,-y; -z,-x,y; -z,x,-y; y,z,x; -y,z,-x; y,-z,-x; -y,-z,x; y,x,-z; -y,-x,-z; y,-x,z; -y,x,z; x,z,-y; -x,z,y; -x,-z,-y; x,-z,y; z,y,-x; z,-y,x; -z,y,x; -z,-y,-x;

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Components

#1: Protein mitochondrial ferritin / / ferritin heavy chain / ferritin H subunit


Mass: 20976.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N4E7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Tris HCL, magnesium chloride, sodium chloride, bicine, sodium azide, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.966 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2002 / Details: mirrors
RadiationMonochromator: W/SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.7→14.9 Å / Num. all: 25592 / Num. obs: 25592 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.084 / Net I/σ(I): 4.91
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1123 / Rsym value: 0.42 / % possible all: 65.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FHA

2fha


Resolution: 1.7→14.9 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1263 -random
Rwork0.17 ---
all0.18 25142 --
obs0.18 25142 87.7 %-
Displacement parametersBiso mean: 16.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 5 210 1607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.57
LS refinement shellResolution: 1.7→1.78 Å
RfactorNum. reflection% reflection
Rfree0.29 2205 -
Rwork0.2 --
obs-2394 68 %

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