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- PDB-8a2m: X-ray structure of Ru(bpy)3]2+ complex (Ru1)-encapsulated human h... -

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Basic information

Entry
Database: PDB / ID: 8a2m
TitleX-ray structure of Ru(bpy)3]2+ complex (Ru1)-encapsulated human heavy chain ferritin
ComponentsFerritin heavy chain, N-terminally processed
KeywordsTRANSPORT PROTEIN / human ferritin / heavy chain / antimicrobial peptide / encapsulation / SDS
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 ion transport / Iron uptake and 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 / cytoplasm / cytosol
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: 1.57 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 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,77119
Polymers21,1821
Non-polymers59018
Water5,873326
1
AAA: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)522,510456
Polymers508,35624
Non-polymers14,154432
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 area93160 Å2
ΔGint-683 kcal/mol
Surface area147200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.770, 183.770, 183.770
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-203-

MG

21AAA-204-

MG

31AAA-212-

CL

41AAA-218-

FE

51AAA-334-

HOH

61AAA-577-

HOH

71AAA-578-

HOH

81AAA-597-

HOH

91AAA-618-

HOH

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Components

#1: Protein Ferritin heavy chain, N-terminally processed


Mass: 21181.512 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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.7 %
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: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.57→106.1 Å / Num. obs: 37411 / % possible obs: 99.4 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.25 / Net I/σ(I): 15
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 15 % / Rmerge(I) obs: 1 / Num. unique obs: 1836 / CC1/2: 0.846 / Rpim(I) all: 0.38 / Rrim(I) all: 0.9 / % 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: 1.57→105.622 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.156 / SU B: 1.235 / SU ML: 0.043 / Average fsc free: 0.9497 / Average fsc work: 0.9544 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1904 1879 5.032 %
Rwork0.1602 35459 -
all0.162 --
obs-37338 99.245 %
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: 21.802 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.57→105.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 18 326 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161411
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6392062
X-RAY DIFFRACTIONr_angle_other_deg1.5741.5933268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15524.1392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.09157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.240.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.21226
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2738
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2790.2195
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.215
X-RAY DIFFRACTIONr_nbd_other0.1810.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3240.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1920.21
X-RAY DIFFRACTIONr_mcbond_it2.0971.937730
X-RAY DIFFRACTIONr_mcbond_other2.0761.931726
X-RAY DIFFRACTIONr_mcangle_it3.2962.884920
X-RAY DIFFRACTIONr_mcangle_other3.282.881919
X-RAY DIFFRACTIONr_scbond_it3.6912.261795
X-RAY DIFFRACTIONr_scbond_other3.6892.262796
X-RAY DIFFRACTIONr_scangle_it5.5973.2641139
X-RAY DIFFRACTIONr_scangle_other5.5973.2651140
X-RAY DIFFRACTIONr_lrange_it7.48825.7051945
X-RAY DIFFRACTIONr_lrange_other6.98423.8111833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.57-1.6110.2751370.22725710.22927130.8890.999.81570.212
1.611-1.6550.2281300.20825300.20926660.9190.92399.77490.188
1.655-1.7030.2171320.20824520.20825910.9360.9399.72980.183
1.703-1.7550.1961170.223850.225140.9470.94299.52270.171
1.755-1.8130.1851080.17923000.17924220.9570.95799.4220.147
1.813-1.8760.2171280.18122390.18323820.9420.95299.37030.149
1.876-1.9470.1961140.17721390.17822750.9480.95299.0330.145
1.947-2.0270.2031220.16720580.16922020.9530.96199.00090.138
2.027-2.1170.1691250.14819710.14921220.9680.97198.77470.122
2.117-2.220.176870.13719120.13820250.9630.97798.7160.118
2.22-2.340.1641070.13718080.13919500.9690.97698.20510.12
2.34-2.4820.173860.14817310.14918390.9660.97198.80370.135
2.482-2.6530.2750.15216340.15417400.960.96898.21840.144
2.653-2.8660.197830.15415200.15616210.9610.96998.88960.151
2.866-3.1390.171830.15314190.15415090.9680.97299.53610.154
3.139-3.5090.186670.1513110.15213820.9770.97499.71060.16
3.509-4.0510.193600.13311610.13512250.9620.97899.67350.156
4.051-4.960.146570.1279980.12810560.9810.98399.90530.157
4.96-7.0070.248380.2048150.2068530.9470.961000.248
7.007-105.6220.269230.2255050.2265340.9440.95598.87640.278

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