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- PDB-8j9l: Crystal Structure of Human H-Ferritin variant 123F assembling in ... -

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Basic information

Entry
Database: PDB / ID: 8j9l
TitleCrystal Structure of Human H-Ferritin variant 123F assembling in solution2
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 uptake and transport / ferrous iron binding / iron ion transport / 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: 2.5 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 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,34628
Polymers255,45312
Non-polymers89416
Water1,17165
1
B: Ferritin heavy chain
C: Ferritin heavy chain
G: Ferritin heavy chain
I: Ferritin heavy chain
K: Ferritin heavy chain
hetero molecules

B: Ferritin heavy chain
C: Ferritin heavy chain
G: Ferritin heavy chain
I: Ferritin heavy chain
K: Ferritin heavy chain
hetero molecules

D: Ferritin heavy chain
H: Ferritin heavy chain
J: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

D: Ferritin heavy chain
H: Ferritin heavy chain
J: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,69356
Polymers510,90624
Non-polymers1,78732
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation17_544x-y+1/3,-y-1/3,-z-1/31
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation15_544-x+y+1/3,-x-1/3,z-1/31
Buried area96320 Å2
ΔGint-690 kcal/mol
Surface area139800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.696, 261.696, 320.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-201-

FE

21D-202-

FE

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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.: 12 / 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.: 16 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 50 mM BICINE pH 9.5, 800 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 EIGER2 S 9M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→29.26 Å / Num. obs: 144447 / % possible obs: 97.24 % / Redundancy: 2 % / CC1/2: 0.412 / Net I/σ(I): 4
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 14354 / CC1/2: 0.702

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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: 2.5→29.26 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 1961 1.39 %
Rwork0.2473 --
obs0.2478 140647 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16992 0 16 65 17073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917352
X-RAY DIFFRACTIONf_angle_d1.09823364
X-RAY DIFFRACTIONf_dihedral_angle_d7.8282244
X-RAY DIFFRACTIONf_chiral_restr0.0532448
X-RAY DIFFRACTIONf_plane_restr0.0063072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.46311080.43767565X-RAY DIFFRACTION75
2.56-2.630.41371330.36719514X-RAY DIFFRACTION93
2.63-2.710.38761400.33299878X-RAY DIFFRACTION98
2.71-2.80.34061390.31569954X-RAY DIFFRACTION99
2.8-2.90.34521430.30510076X-RAY DIFFRACTION99
2.9-3.010.32061410.28269993X-RAY DIFFRACTION99
3.01-3.150.29831440.272910158X-RAY DIFFRACTION100
3.15-3.320.32481470.259110125X-RAY DIFFRACTION100
3.32-3.520.26621400.235910152X-RAY DIFFRACTION100
3.52-3.790.28221400.212910163X-RAY DIFFRACTION100
3.79-4.170.24481440.192410199X-RAY DIFFRACTION100
4.18-4.780.22741430.166710206X-RAY DIFFRACTION100
4.78-6.010.24271460.190810256X-RAY DIFFRACTION100
6.01-29.260.18251530.176810447X-RAY DIFFRACTION100

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