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- PDB-5gn8: Structure of a 48-mer protein nanocage fabricated from its 24-mer... -

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Basic information

Entry
Database: PDB / ID: 5gn8
TitleStructure of a 48-mer protein nanocage fabricated from its 24-mer analogue by subunit interface redesign
Components(Ferritin heavy chain) x 2
KeywordsOXIDOREDUCTASE / ferritin / nanocage / subunit interface redesign
Function / homology
Function and homology information


iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / 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, 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: 2.805 Å
AuthorsZhang, S. / Zang, J. / Zhao, G. / Mikami, B.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: ACS Nano / Year: 2016
Title: "Silent" Amino Acid Residues at Key Subunit Interfaces Regulate the Geometry of Protein Nanocages
Authors: Zhang, S. / Zang, J. / Zhang, X. / Chen, H. / Mikami, B. / Zhao, G.
History
DepositionJul 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.3Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7054
Polymers37,6252
Non-polymers802
Water362
1
A: Ferritin heavy chain
B: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)904,92196
Polymers902,99748
Non-polymers1,92448
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area159740 Å2
ΔGint-1163 kcal/mol
Surface area295730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.120, 236.120, 236.120
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-301-

HOH

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Components

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


Mass: 20453.725 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 (E. coli) / References: UniProt: P02794, ferroxidase
#2: Protein Ferritin heavy chain / / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 17171.166 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 (E. coli) / References: UniProt: P02794, ferroxidase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 300 K / Method: vapor diffusion
Details: 0.1 M imidazol-HCl at pH 7.5, 10% reagent alcohol (15%) and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13673 / % possible obs: 99.9 % / Redundancy: 1.2 % / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FHA

1fha


Resolution: 2.805→41.741 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.65
RfactorNum. reflection% reflection
Rfree0.2512 725 5.04 %
Rwork0.2134 --
obs0.2153 13659 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.805→41.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 2 2 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012576
X-RAY DIFFRACTIONf_angle_d0.8953471
X-RAY DIFFRACTIONf_dihedral_angle_d19.608967
X-RAY DIFFRACTIONf_chiral_restr0.067362
X-RAY DIFFRACTIONf_plane_restr0.004457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8054-3.02190.41511520.3312646X-RAY DIFFRACTION100
3.0219-3.32590.3291510.28222660X-RAY DIFFRACTION100
3.3259-3.80690.28361190.24122723X-RAY DIFFRACTION100
3.8069-4.79520.21871570.19012701X-RAY DIFFRACTION100
4.7952-41.74510.22051460.18612923X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.70260.201-0.07430.6639-1.47852.7942-0.20970.107-0.5345-0.42360.34890.4330.9540.07950.00040.8019-0.0541-0.16120.8913-0.11260.910853.880497.629286.5868
20.58821.25960.13131.14950.40182.2844-0.047-0.3466-0.1939-0.17590.473-0.34830.24960.2609-0.00020.6079-0.0047-0.1760.9357-0.05540.827157.5454105.83893.5085
3-0.1986-0.1987-0.07320.0592-0.0124-0.133-0.47991.00310.052-0.3471-0.3162-0.8580.5796-0.11230.00081.11470.0739-0.0930.95330.04470.974859.055793.878277.6723
42.0812.01970.42571.0523-0.69963.1280.05890.3204-0.1428-0.6532-0.11490.18110.5183-0.2163-0.00010.7758-0.1034-0.18741.03470.01140.926746.845998.596993.6131
50.05950.04430.03770.01310.0120.05971.1751-0.84940.1386-0.15580.8659-0.31990.3561-0.9519-0.00012.7559-0.18060.06622.74270.05151.892165.828580.394691.9861
61.13990.5511.6472.935-3.51415.284-0.03460.9293-0.97360.1698-0.72550.33340.8395-0.14330.00310.5402-0.0939-0.14920.9308-0.10391.146250.086499.5447104.684
70.14180.2562-0.10140.1599-0.04790.39310.64930.74590.3679-0.7598-0.43710.63350.01450.42090.00070.4754-0.0143-0.05380.98910.02560.891849.0312114.7614110.1741
81.53850.940.24641.1313-0.44532.0385-0.06840.1213-0.0993-0.4199-0.03970.49090.1119-0.02950.00080.64250.0349-0.2190.96390.01760.713154.613116.587180.5188
90.464-0.08181.03492.2987-0.8051.1325-0.2355-0.14690.2151-0.48250.2944-0.77860.16010.1552-0.00080.72170.0343-0.09740.9335-0.04130.949565.2256110.728482.727
101.17851.2897-0.23131.5619-1.68763.3030.0330.7282-0.0666-0.7959-0.01370.23260.1655-0.03740.00020.81930.0433-0.19161.1775-0.05850.739658.8116114.177672.4701
111.07681.4871-0.74781.4151-1.34351.0982-0.134-0.4740.04310.079-0.0935-0.427-0.41390.1511-0.00060.84380.0573-0.14511.0907-0.05680.921763.7473127.778180.1499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 121 )
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 157 )
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 171 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 76 )
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 123 )
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 146 )

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