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- PDB-8kh2: Crystal structure of horse-spleen L-ferritin fused with amyloid b... -

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Basic information

Entry
Database: PDB / ID: 8kh2
TitleCrystal structure of horse-spleen L-ferritin fused with amyloid beta peptide (1-42).
ComponentsFerritin light chain,Amyloid-beta precursor protein (Fragment)
KeywordsMETAL BINDING PROTEIN / Ferritin cage / Amyloid beta fusion
Function / homology
Function and homology information


ferritin complex / Golgi-associated vesicle / autolysosome / clathrin-coated pit / ferric iron binding / autophagosome / ferrous iron binding / recycling endosome / cognition / iron ion transport ...ferritin complex / Golgi-associated vesicle / autolysosome / clathrin-coated pit / ferric iron binding / autophagosome / ferrous iron binding / recycling endosome / cognition / iron ion transport / growth cone / cytoplasmic vesicle / perikaryon / intracellular iron ion homeostasis / early endosome / iron ion binding / cell surface / extracellular region / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Amyloidogenic glycoprotein / 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. ...Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Amyloidogenic glycoprotein / 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 light chain / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaity, B. / Tian, J. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biomater Sci / Year: 2024
Title: Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage.
Authors: Maity, B. / Kameyama, S. / Tian, J. / Pham, T.T. / Abe, S. / Chatani, E. / Murata, K. / Ueno, T.
History
DepositionAug 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin light chain,Amyloid-beta precursor protein (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,88114
Polymers24,5461
Non-polymers1,33513
Water2,972165
1
A: Ferritin light chain,Amyloid-beta precursor protein (Fragment)
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)621,144336
Polymers589,09624
Non-polymers32,048312
Water43224
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 area99670 Å2
ΔGint-1151 kcal/mol
Surface area142090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.935, 181.935, 181.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-303-

CD

21A-304-

CD

31A-305-

CD

41A-311-

SO4

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Components

#1: Protein Ferritin light chain,Amyloid-beta precursor protein (Fragment)


Mass: 24545.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL, APP / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791, UniProt: Q28280
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate (12-20 mM)

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Data collection

DiffractionMean temperature: 93.1 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→21.691 Å / Num. obs: 17564 / % possible obs: 97.7 % / Redundancy: 7.4 % / CC1/2: 0.996 / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1264 / CC1/2: 0.977

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.691 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.171 / SU B: 3.785 / SU ML: 0.104 / Average fsc free: 0.9562 / Average fsc work: 0.9656 / Cross valid method: FREE R-VALUE / ESU R: 0.174 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2581 913 5.201 %
Rwork0.2152 16641 -
all0.217 --
obs-17554 97.414 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.437 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→21.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 25 165 1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161388
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.6471955
X-RAY DIFFRACTIONr_angle_other_deg0.6531.5763189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.106512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95810268
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1121075
X-RAY DIFFRACTIONr_chiral_restr0.10.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined0.2460.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21161
X-RAY DIFFRACTIONr_nbtor_refined0.190.2698
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3010.218
X-RAY DIFFRACTIONr_nbd_other0.150.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.239
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1780.22
X-RAY DIFFRACTIONr_mcbond_it1.9541.213695
X-RAY DIFFRACTIONr_mcbond_other1.9541.213695
X-RAY DIFFRACTIONr_mcangle_it3.0312.162870
X-RAY DIFFRACTIONr_mcangle_other3.0312.162871
X-RAY DIFFRACTIONr_scbond_it3.5531.585749
X-RAY DIFFRACTIONr_scbond_other3.5541.569738
X-RAY DIFFRACTIONr_scangle_it5.6622.7211079
X-RAY DIFFRACTIONr_scangle_other5.6692.6911062
X-RAY DIFFRACTIONr_lrange_it6.89714.4141736
X-RAY DIFFRACTIONr_lrange_other6.72213.3071686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.269560.19611990.19912760.9530.97698.35420.158
2.052-2.1070.201730.18911630.1912620.9740.97897.93980.157
2.107-2.1680.224750.20711220.20812200.9650.96798.11480.174
2.168-2.2340.537510.59420.50211910.8840.88583.37530.348
2.234-2.3060.59490.5549840.55611540.8170.83589.51470.506
2.306-2.3860.284450.21810730.2211210.9550.9799.73240.164
2.386-2.4750.184530.1710250.1710790.9790.98299.90730.137
2.475-2.5750.286450.15510160.1610610.9490.9851000.123
2.575-2.6870.166560.1399410.1419980.9830.98999.89980.11
2.687-2.8160.216590.1528980.1579590.9780.98599.79150.117
2.816-2.9660.257460.168880.1659350.9670.98399.8930.13
2.966-3.1420.212500.1668230.1698730.9750.9831000.138
3.142-3.3540.212490.1957740.1968230.9740.9781000.171
3.354-3.6160.265370.2077290.217880.9560.97497.20810.163
3.616-3.950.268490.2096740.2137290.9630.97599.1770.185
3.95-4.3980.18340.156220.1516640.980.98798.79520.127
4.398-5.0440.175280.1325700.1335990.9840.9999.83310.116
5.044-6.0960.306210.1945090.1975310.9650.98299.81170.164
6.096-8.2990.259230.1944050.1974280.9690.9781000.168
8.299-21.6910.193140.2132840.2123000.9820.97599.33330.199

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