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- PDB-8a5n: X-ray structure of human H-chain ferritin treated with SDS -

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Basic information

Entry
Database: PDB / ID: 8a5n
TitleX-ray structure of human H-chain ferritin treated with SDS
ComponentsFerritin heavy chain
KeywordsTRANSPORT PROTEIN / ferritin / nanocage / disassembly / reassembly / sodium dodecyl sulphate
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / iron ion transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / 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 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2023
Title: A new and efficient procedure to load bioactive molecules within the human heavy-chain ferritin nanocage.
Authors: Lucignano, R. / Stanzione, I. / Ferraro, G. / Di Girolamo, R. / Cane, C. / Di Somma, A. / Duilio, A. / Merlino, A. / Picone, D.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,87023
Polymers21,1241
Non-polymers74622
Water6,395355
1
AAA: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)524,879552
Polymers506,98724
Non-polymers17,892528
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area97560 Å2
ΔGint-680 kcal/mol
Surface area150560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.920, 183.920, 183.920
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
11AAA-211-

CL

21AAA-213-

MG

31AAA-214-

MG

41AAA-222-

MG

51AAA-334-

HOH

61AAA-583-

HOH

71AAA-629-

HOH

81AAA-636-

HOH

91AAA-643-

HOH

101AAA-645-

HOH

111AAA-655-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21124.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02794, ferroxidase

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Non-polymers , 5 types, 377 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 59.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0 M magnesium chloride 0.1 M bicine buffer pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.52→106.18 Å / Num. obs: 41266 / % possible obs: 99.5 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.016 / Rrim(I) all: 0.185 / Net I/σ(I): 41.2
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2030 / CC1/2: 0.859 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N27

5n27


Resolution: 1.52→106.18 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.091 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 2056 4.982 %
Rwork0.1513 39210 -
all0.153 --
obs-41266 99.489 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.741 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→106.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 27 355 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161453
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.6392142
X-RAY DIFFRACTIONr_angle_other_deg1.6071.5923370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74123.9898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.723158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2540.2395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21201
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.213
X-RAY DIFFRACTIONr_nbd_other0.1830.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.470.261
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_mcbond_it2.2821.989752
X-RAY DIFFRACTIONr_mcbond_other2.251.982748
X-RAY DIFFRACTIONr_mcangle_it3.4612.966955
X-RAY DIFFRACTIONr_mcangle_other3.4452.964954
X-RAY DIFFRACTIONr_scbond_it3.592.322828
X-RAY DIFFRACTIONr_scbond_other3.5882.324829
X-RAY DIFFRACTIONr_scangle_it5.4483.3521183
X-RAY DIFFRACTIONr_scangle_other5.4463.3541184
X-RAY DIFFRACTIONr_lrange_it8.14127.3372015
X-RAY DIFFRACTIONr_lrange_other7.7525.6241919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5590.2271530.2162825X-RAY DIFFRACTION99.8994
1.559-1.6020.2391590.2062779X-RAY DIFFRACTION99.864
1.602-1.6490.2081520.1862691X-RAY DIFFRACTION99.7194
1.649-1.6990.2081380.1922634X-RAY DIFFRACTION99.8559
1.699-1.7550.2011300.1822548X-RAY DIFFRACTION99.7765
1.755-1.8170.2061140.1762508X-RAY DIFFRACTION99.7717
1.817-1.8850.1741230.1612355X-RAY DIFFRACTION99.12
1.885-1.9620.1861060.1562308X-RAY DIFFRACTION99.1376
1.962-2.0490.1751290.1462186X-RAY DIFFRACTION99.0586
2.049-2.1490.189930.142114X-RAY DIFFRACTION98.6148
2.149-2.2660.1721040.1312008X-RAY DIFFRACTION99.0155
2.266-2.4030.1711010.1311925X-RAY DIFFRACTION98.8293
2.403-2.5690.1591010.1321781X-RAY DIFFRACTION99.0005
2.569-2.7740.158880.1391697X-RAY DIFFRACTION99.3322
2.774-3.0390.163770.1431569X-RAY DIFFRACTION99.7576
3.039-3.3970.164830.131439X-RAY DIFFRACTION99.8033
3.397-3.9220.165550.1351288X-RAY DIFFRACTION100
3.922-4.8020.176630.1161108X-RAY DIFFRACTION100
4.802-6.7840.204500.196883X-RAY DIFFRACTION100

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