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- PDB-6ipp: Non-native ferritin 8-mer mutant-C90A/C102A/C130A/D144C -

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Basic information

Entry
Database: PDB / ID: 6ipp
TitleNon-native ferritin 8-mer mutant-C90A/C102A/C130A/D144C
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / ferritin / cysteine
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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsZang, J. / Chen, H. / Zhou, K. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31730069 China
CitationJournal: Nat Commun / Year: 2019
Title: Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages.
Authors: Zang, J. / Chen, H. / Zhang, X. / Zhang, C. / Guo, J. / Du, M. / Zhao, G.
History
DepositionNov 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7473
Polymers40,6912
Non-polymers561
Water95553
1
A: Ferritin heavy chain
B: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)977,92872
Polymers976,58848
Non-polymers1,34024
Water86548
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 area148900 Å2
ΔGint-878 kcal/mol
Surface area300630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.374, 235.374, 235.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

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


Mass: 20345.584 Da / Num. of mol.: 2 / Mutation: C90A/C102A/C130A/D144C
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.: 1 / Source method: isolated from a natural source / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 293.17 K / Method: evaporation / pH: 7 / Details: Sodium chloride,MPD,TRIS

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.699→48.05 Å / Num. obs: 15943 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 1 / Rmerge(I) obs: 0.1944 / Net I/σ(I): 6.5
Reflection shellResolution: 2.699→3.105 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHA

2fha


Resolution: 2.699→48.046 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2321 792 4.97 %
Rwork0.1944 --
obs0.1962 15943 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.699→48.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 1 53 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012547
X-RAY DIFFRACTIONf_angle_d0.9973432
X-RAY DIFFRACTIONf_dihedral_angle_d18.9011535
X-RAY DIFFRACTIONf_chiral_restr0.053359
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6985-2.86760.30361290.23732460X-RAY DIFFRACTION100
2.8676-3.08890.28311410.22832442X-RAY DIFFRACTION100
3.0889-3.39970.26451320.2122475X-RAY DIFFRACTION100
3.3997-3.89150.22141330.18862505X-RAY DIFFRACTION100
3.8915-4.90210.18191210.16162553X-RAY DIFFRACTION100
4.9021-48.05310.21811360.19422716X-RAY DIFFRACTION100

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