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- PDB-9jgp: Structure of Pd ions bound to human heavy chain ferritin nanocage. -

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Basic information

Entry
Database: PDB / ID: 9jgp
TitleStructure of Pd ions bound to human heavy chain ferritin nanocage.
ComponentsFerritin heavy chain, N-terminally processed
KeywordsAPOPTOSIS / granzyme B / nanovesicles / ferritin / Palladium
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
PALLADIUM ION / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLiu, Y.J. / Zhao, M. / Hu, X.Y. / Kang, H.L. / Liu, Q.Q. / Huang, X.L.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271448 China
National Natural Science Foundation of China (NSFC)82072054 China
National Natural Science Foundation of China (NSFC)21877065 China
National Natural Science Foundation of China (NSFC)82111530210 China
CitationJournal: To Be Published
Title: Structure of Pd ions bound to human heavy chain ferritin nanocage.
Authors: Hu, X.Y. / Kang, H.L. / Liu, Q.Q. / Zhao, M. / Li, Y.K. / Peng, W.C. / Qi, T.Y. / Liu, R.M. / Jiao, L. / Dou, H.J. / Zhuang, J. / Liu, Y.J. / Mann, S. / Huang, X.L.
History
DepositionSep 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,42011
Polymers21,0181
Non-polymers40210
Water3,027168
1
A: Ferritin heavy chain, N-terminally processed
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)514,085264
Polymers504,43724
Non-polymers9,648240
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 area96100 Å2
ΔGint-800 kcal/mol
Surface area140310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.700, 183.700, 183.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-206-

MG

21A-207-

MG

31A-210-

PD

41A-306-

HOH

51A-468-

HOH

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Components

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


Mass: 21018.205 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 phage EcSzw-2 (virus) / References: UniProt: P02794
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 106.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 59.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2 M MgCl2, 0.1 M Bicine, pH 9.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.53→30.62 Å / Num. obs: 40487 / % possible obs: 99.95 % / Redundancy: 76.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2373 / Rrim(I) all: 0.2388 / Net I/σ(I): 15.52
Reflection shellResolution: 1.53→1.585 Å / Rmerge(I) obs: 2.943 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3968 / CC1/2: 0.775 / Rrim(I) all: 2.966

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→30.62 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 1929 4.76 %
Rwork0.1727 --
obs0.1733 40483 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 10 168 1587

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