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- PDB-8jai: Crystal Structure of Human H-Ferritin variant 123F assembling in ... -

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Basic information

Entry
Database: PDB / ID: 8jai
TitleCrystal Structure of Human H-Ferritin variant 123F assembling in solution 1
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / protein assembly
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 / 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: 2.56 Å
AuthorsChen, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Sci / Year: 2023
Title: Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular pi-pi Interactions.
Authors: Chen, X. / Zhang, T. / Liu, H. / Zang, J. / Lv, C. / Du, M. / Zhao, G.
History
DepositionMay 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 31, 2024Provider: 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
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,91142
Polymers510,90624
Non-polymers1,00518
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area94790 Å2
ΔGint-509 kcal/mol
Surface area148500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)301.660, 301.660, 316.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 21287.742 Da / Num. of mol.: 24 / Mutation: D123F
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 (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 50 mM CAPS pH 9.5, 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.56→65.59 Å / Num. obs: 231274 / % possible obs: 99.89 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 7.56
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 22913 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→65.59 Å / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 47.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3684 11622 7.43 %
Rwork0.3345 --
obs-231274 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→65.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33981 0 18 2 34001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01234701
X-RAY DIFFRACTIONf_angle_d1.28946725
X-RAY DIFFRACTIONf_dihedral_angle_d11.4914488
X-RAY DIFFRACTIONf_chiral_restr0.0594896
X-RAY DIFFRACTIONf_plane_restr0.0076144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.60.39426070.35510884X-RAY DIFFRACTION95
2.6-2.650.37665980.35510834X-RAY DIFFRACTION95
2.65-2.70.39436430.359410823X-RAY DIFFRACTION94
2.7-2.760.34665870.346610888X-RAY DIFFRACTION95
2.76-2.820.3935680.345510914X-RAY DIFFRACTION95
2.82-2.880.37745740.34810932X-RAY DIFFRACTION95
2.88-2.960.38215720.346810925X-RAY DIFFRACTION95
2.96-3.040.37685620.344210885X-RAY DIFFRACTION95
3.04-3.120.37915380.341611001X-RAY DIFFRACTION95
3.12-3.230.38545580.330910929X-RAY DIFFRACTION95
3.23-3.340.38325870.327810951X-RAY DIFFRACTION95
3.34-3.470.36816550.323510878X-RAY DIFFRACTION94
3.47-3.630.33515830.312510935X-RAY DIFFRACTION95
3.63-3.820.31895560.295411006X-RAY DIFFRACTION95
3.82-4.060.33216010.291510985X-RAY DIFFRACTION95
4.06-4.380.30315660.28211033X-RAY DIFFRACTION95
4.38-4.820.28455560.271811070X-RAY DIFFRACTION95
4.82-5.510.30715650.282911096X-RAY DIFFRACTION95
5.51-6.950.33495590.303111213X-RAY DIFFRACTION95
6.95-65.590.32125930.287511464X-RAY DIFFRACTION95

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