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- PDB-8a2l: X-ray structure of TRIL-encapsulated human heavy chain ferritin -

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Basic information

Entry
Database: PDB / ID: 8a2l
TitleX-ray structure of TRIL-encapsulated human heavy chain ferritin
ComponentsFerritin heavy chain
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: 2.301 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,55914
Polymers21,1241
Non-polymers43513
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-58 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.060, 183.060, 183.060
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-204-

CL

21AAA-206-

MG

31AAA-207-

MG

41AAA-212-

FE

51AAA-424-

HOH

61AAA-462-

HOH

71AAA-466-

HOH

81AAA-471-

HOH

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Components

#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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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.: 171 / 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: 3.02 Å3/Da / Density % sol: 59.34 %
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: 1.0001 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: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.3→105.69 Å / Num. obs: 12183 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.059 / Net I/av σ(I): 13 / Net I/σ(I): 0.711
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 15 % / Rmerge(I) obs: 1.8 / Num. unique obs: 607 / CC1/2: 0.827 / Rpim(I) all: 0.371 / Rrim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5n27

5n27


Resolution: 2.301→105.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.106 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.228 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2236 603 4.95 %
Rwork0.1706 11580 -
all0.173 --
obs-12183 99.787 %
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: 34.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.301→105.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 13 171 1608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161358
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6372000
X-RAY DIFFRACTIONr_angle_other_deg1.3861.593134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75623.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.124158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_nbd_refined0.2070.2337
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.21175
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2712
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.293
X-RAY DIFFRACTIONr_metal_ion_refined0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.213
X-RAY DIFFRACTIONr_nbd_other0.1670.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.229
X-RAY DIFFRACTIONr_mcbond_it3.0173.376710
X-RAY DIFFRACTIONr_mcbond_other2.9533.369708
X-RAY DIFFRACTIONr_mcangle_it4.855.039891
X-RAY DIFFRACTIONr_mcangle_other4.7995.037891
X-RAY DIFFRACTIONr_scbond_it3.7153.794772
X-RAY DIFFRACTIONr_scbond_other3.7133.795773
X-RAY DIFFRACTIONr_scangle_it6.0385.531109
X-RAY DIFFRACTIONr_scangle_other6.0375.5311110
X-RAY DIFFRACTIONr_lrange_it9.04439.9151754
X-RAY DIFFRACTIONr_lrange_other9.0439.5431719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.3610.23420.229829X-RAY DIFFRACTION99.8853
2.361-2.4250.26260.227821X-RAY DIFFRACTION99.7644
2.425-2.4960.235410.223797X-RAY DIFFRACTION100
2.496-2.5720.241300.207767X-RAY DIFFRACTION99.7497
2.572-2.6570.233390.188750X-RAY DIFFRACTION99.8734
2.657-2.750.215520.178708X-RAY DIFFRACTION100
2.854-2.970.253340.175686X-RAY DIFFRACTION99.8613
2.97-3.1020.259410.165645X-RAY DIFFRACTION99.8544
3.102-3.2530.232320.153626X-RAY DIFFRACTION99.8483
3.253-3.4290.193270.141596X-RAY DIFFRACTION99.2038
3.429-3.6370.214380.129550X-RAY DIFFRACTION99.661
3.637-3.8880.178210.129547X-RAY DIFFRACTION99.4746
3.888-4.1990.155330.124490X-RAY DIFFRACTION99.619
4.199-4.5990.192250.135472X-RAY DIFFRACTION99.7992
4.599-5.140.252300.154420X-RAY DIFFRACTION100
5.14-5.9330.265200.213390X-RAY DIFFRACTION100
5.933-7.2610.33280.179342X-RAY DIFFRACTION100

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