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- PDB-8pp3: Binary crystal structure of positively supercharged ferritin vari... -

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Basic information

Entry
Database: PDB / ID: 8pp3
TitleBinary crystal structure of positively supercharged ferritin variant Ftn(pos) and crystal contact tuned negatively supercharged ferritin variant Ftn(neg)-m1 (Mg formate condition)
Components(Ferritin heavy ...) x 2
KeywordsOXIDOREDUCTASE / protein design / protein engineering / protein interfaces / superlattice / nanocage / ferritin / protein container / charged nanocage
Function / homology
Function and homology information


iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / 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 / membrane / 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 / 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 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLang, L. / Beck, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)2056 Germany
CitationJournal: Biomacromolecules / Year: 2024
Title: Assembly Requirements for the Construction of Large-Scale Binary Protein Structures.
Authors: Lang, L. / Bohler, H. / Wagler, H. / Beck, T.
History
DepositionJul 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,86830
Polymers256,78112
Non-polymers1,08718
Water17,583976
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,79664
Polymers515,98224
Non-polymers2,81440
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area99310 Å2
ΔGint-671 kcal/mol
Surface area146320 Å2
MethodPISA
2
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,67556
Polymers511,14024
Non-polymers1,53532
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area95730 Å2
ΔGint-720 kcal/mol
Surface area139460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.007, 127.007, 175.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11B-384-

HOH

21C-388-

HOH

31L-356-

HOH

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Components

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Ferritin heavy ... , 2 types, 12 molecules ABCDEFGHIJKL

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


Mass: 21499.246 Da / Num. of mol.: 6
Mutation: A18K, C90K, N98R, C102K, H105K N25R, N109K, D123K, E162R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pet22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: P02794, ferroxidase
#2: Protein
Ferritin heavy chain / / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21297.514 Da / Num. of mol.: 6 / Mutation: C90E, C102E, H105E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pet22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: P02794, ferroxidase

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Non-polymers , 4 types, 994 molecules

#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 976 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir: 0.19M Magnesium FormateFtn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaClFtn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to ...Details: reservoir: 0.19M Magnesium FormateFtn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaClFtn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to coverslide in this order.
Temp details: held stable

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→72.1 Å / Num. obs: 391240 / % possible obs: 97.7 % / Redundancy: 12.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Net I/σ(I): 8.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.7 % / Num. unique obs: 16153 / CC1/2: 0.135

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Processing

Software
NameVersionClassification
xia2data reduction
XDSdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→59.774 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.022 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2413 16135 4.124 %
Rwork0.2185 375076 -
all0.22 --
obs-391211 97.689 %
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: 24.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.518 Å2-0 Å2-0 Å2
2---0.518 Å2-0 Å2
3---1.036 Å2
Refinement stepCycle: LAST / Resolution: 1.55→59.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17100 0 38 976 18114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01317559
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616396
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.64123600
X-RAY DIFFRACTIONr_angle_other_deg1.3991.59237817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82452071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02723.4661102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.733153331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.64915105
X-RAY DIFFRACTIONr_chiral_restr0.0780.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024134
X-RAY DIFFRACTIONr_nbd_refined0.210.23686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.214680
X-RAY DIFFRACTIONr_nbtor_refined0.1640.28428
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.27665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2861
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.27
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.244
X-RAY DIFFRACTIONr_nbd_other0.1770.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.289
X-RAY DIFFRACTIONr_mcbond_it1.6872.3898293
X-RAY DIFFRACTIONr_mcbond_other1.6852.3888291
X-RAY DIFFRACTIONr_mcangle_it2.2133.57510361
X-RAY DIFFRACTIONr_mcangle_other2.2113.57510361
X-RAY DIFFRACTIONr_scbond_it2.6212.7059266
X-RAY DIFFRACTIONr_scbond_other2.6212.7069267
X-RAY DIFFRACTIONr_scangle_it3.9733.9413239
X-RAY DIFFRACTIONr_scangle_other3.9733.9413240
X-RAY DIFFRACTIONr_lrange_it4.74228.07220106
X-RAY DIFFRACTIONr_lrange_other4.73327.97719938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5900.36824524X-RAY DIFFRACTION82.9775
1.59-1.63300.3626080X-RAY DIFFRACTION90.3548
1.633-1.6810.3664510.34726366X-RAY DIFFRACTION95.8983
1.681-1.7320.32412790.3225791X-RAY DIFFRACTION99.2884
1.732-1.7890.30413300.28225066X-RAY DIFFRACTION99.9092
1.789-1.8520.28412120.25124276X-RAY DIFFRACTION99.9922
1.852-1.9220.28512440.23423419X-RAY DIFFRACTION99.9554
1.922-20.26211970.2222522X-RAY DIFFRACTION99.9831
2-2.0890.24511990.20721557X-RAY DIFFRACTION99.9605
2.089-2.1910.24211300.220621X-RAY DIFFRACTION99.9724
2.191-2.310.25110550.19919598X-RAY DIFFRACTION99.9806
2.31-2.450.2299540.19518639X-RAY DIFFRACTION99.9796
2.45-2.6190.2339160.19717451X-RAY DIFFRACTION99.9837
2.619-2.8290.2248400.20216318X-RAY DIFFRACTION99.9883
2.829-3.0990.2248260.20514963X-RAY DIFFRACTION99.943
3.099-3.4640.2387270.21213511X-RAY DIFFRACTION99.986
3.464-40.226000.19912020X-RAY DIFFRACTION99.9762
4-4.8980.2185220.18810155X-RAY DIFFRACTION99.9906
4.898-6.9240.243890.2257868X-RAY DIFFRACTION99.9637
6.924-59.7740.2562640.224331X-RAY DIFFRACTION99.7828

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