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- PDB-5znd: 8-mer nanotube derived from 24-mer rHuHF nanocage -

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Basic information

Entry
Database: PDB / ID: 5znd
Title8-mer nanotube derived from 24-mer rHuHF nanocage
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / Ferritin / rHuHF / protein redesign / nanotube
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / 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 / membrane / 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: 3 Å
AuthorsWang, W.M. / Wang, L.L. / Zang, J.C. / Chen, H. / Zhao, G.H. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21601112, 21671125 China
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Selective Elimination of the Key Subunit Interfaces Facilitates Conversion of Native 24-mer Protein Nanocage into 8-mer Nanorings.
Authors: Wang, W. / Wang, L. / Chen, H. / Zang, J. / Zhao, X. / Zhao, G. / Wang, H.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 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


Theoretical massNumber of molelcules
Total (without water)15,7631
Polymers15,7631
Non-polymers00
Water21612
1
A: Ferritin heavy chain
x 8


Theoretical massNumber of molelcules
Total (without water)126,1018
Polymers126,1018
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation5_557-x,y,-z+21
crystal symmetry operation6_577x,-y+2,-z+21
crystal symmetry operation7_467y-1,x+1,-z+21
crystal symmetry operation8_667-y+1,-x+1,-z+21
Buried area20970 Å2
ΔGint-102 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.352, 100.352, 51.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

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Components

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


Mass: 15762.584 Da / Num. of mol.: 1 / Mutation: K86Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.06 Å3/Da / Density % sol: 40.43 % / Description: needle like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M ammonium citrate (pH=8.0), 0.1M Tris-HCl (pH=8.0), 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 2556 / % possible obs: 90.1 % / Redundancy: 11.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.124 / Net I/σ(I): 19.58
Reflection shellResolution: 3→3.05 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 6.15 / Num. unique obs: 134 / CC1/2: 0.96 / % possible all: 100

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Processing

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

2fha


Resolution: 3→33.894 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 252 9.96 %
Rwork0.2268 --
obs0.2323 2531 89.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→33.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 12 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031003
X-RAY DIFFRACTIONf_angle_d0.6711350
X-RAY DIFFRACTIONf_dihedral_angle_d23.339611
X-RAY DIFFRACTIONf_chiral_restr0.04140
X-RAY DIFFRACTIONf_plane_restr0.002180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9997-3.77850.33021160.23131065X-RAY DIFFRACTION86
3.7785-33.89650.25761360.2251214X-RAY DIFFRACTION93

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