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- PDB-7cpc: His-Mediated Reversible Self-assembly of Ferritin Nanocage with N... -

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Basic information

Entry
Database: PDB / ID: 7cpc
TitleHis-Mediated Reversible Self-assembly of Ferritin Nanocage with Ni binding
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Assembly / Ni binding
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
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
: / NICKEL (II) ION / Ferritin
Similarity search - Component
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsGu, C. / Zhang, T. / Zhao, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: Acs Nano / Year: 2020
Title: His-Mediated Reversible Self-Assembly of Ferritin Nanocages through Two Different Switches for Encapsulation of Cargo Molecules.
Authors: Gu, C. / Zhang, T. / Lv, C. / Liu, Y. / Wang, Y. / Zhao, G.
History
DepositionAug 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,09818
Polymers118,4106
Non-polymers68712
Water18010
1
A: Ferritin
C: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

B: Ferritin
D: Ferritin
E: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,39072
Polymers473,64124
Non-polymers2,74948
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation7_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation8_444y-1/2,-x-1/2,z-1/21
Buried area94850 Å2
ΔGint-607 kcal/mol
Surface area139340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.845, 125.845, 176.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-202-

NI

31E-201-

NI

41E-202-

NI

51E-301-

HOH

61E-303-

HOH

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Components

#1: Protein
Ferritin


Mass: 19735.049 Da / Num. of mol.: 6 / Mutation: Q89R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: T2B7E1, ferroxidase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 1.26 M (NH4)2SO4, 100 mM Tris (pH =8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 33438 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.959 / Net I/σ(I): 7.545
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 1668 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KH1

6kh1


Resolution: 2.801→36.275 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 2007 6.01 %
Rwork0.1945 31375 -
obs0.199 33382 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 27.4982 Å2 / Biso min: 7.96 Å2
Refinement stepCycle: final / Resolution: 2.801→36.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 12 10 8254
Biso mean--45.85 27.61 -
Num. residues----1002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.801-2.8710.30931370.2062224399
2.871-2.94860.30651410.21392236100
2.9486-3.03530.30491280.23172241100
3.0353-3.13320.35251570.2339227199
3.1332-3.24520.3541460.23112226100
3.2452-3.3750.28811370.21382231100
3.375-3.52850.30351570.21022247100
3.5285-3.71430.37841430.2765221298
3.7143-3.94680.23361450.1959225399
3.9468-4.25110.23271440.1641224299
4.2511-4.67810.19961440.14272254100
4.6781-5.35320.22471430.1558224399
5.3532-6.73740.27581370.1998225799
6.7374-36.2750.19951480.1508221996

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