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- PDB-8pp2: Binary crystal structure of positively supercharged ferritin vari... -

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Basic information

Entry
Database: PDB / ID: 8pp2
TitleBinary crystal structure of positively supercharged ferritin variant Ftn(pos) and native(K86Q) human heavy chain ferritin (Mg formate condition)
Components(Ferritin heavy chain, N-terminally ...) x 2
KeywordsOXIDOREDUCTASE / protein design / charged protein container / binary protein structures / self-assembly / binary nanocage assembly
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / 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 / 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: 2.001 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, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,13035
Polymers242,85412
Non-polymers1,27623
Water12,611700
1
A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules

A: Ferritin heavy chain, N-terminally processed
B: Ferritin heavy chain, N-terminally processed
C: Ferritin heavy chain, N-terminally processed
D: Ferritin heavy chain, N-terminally processed
E: Ferritin heavy chain, N-terminally processed
F: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,11780
Polymers488,64324
Non-polymers3,47456
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 area100020 Å2
ΔGint-643 kcal/mol
Surface area144010 Å2
MethodPISA
2
G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
hetero molecules

G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
hetero molecules

G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
hetero molecules

G: Ferritin heavy chain, N-terminally processed
H: Ferritin heavy chain, N-terminally processed
I: Ferritin heavy chain, N-terminally processed
J: Ferritin heavy chain, N-terminally processed
K: Ferritin heavy chain, N-terminally processed
L: Ferritin heavy chain, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,40460
Polymers482,77224
Non-polymers1,63236
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 area96020 Å2
ΔGint-630 kcal/mol
Surface area139780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.802, 126.802, 175.598
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
11C-382-

HOH

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Components

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Ferritin heavy chain, N-terminally ... , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferritin heavy chain, N-terminally processed


Mass: 20360.135 Da / Num. of mol.: 6
Mutation: K86Q, 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 BL21(DE3) (bacteria) / References: UniProt: P02794
#2: Protein
Ferritin heavy chain, N-terminally processed


Mass: 20115.494 Da / Num. of mol.: 6 / 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 / Plasmid: pet22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02794

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Non-polymers , 4 types, 723 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir: 0.19M Magnesium Formate Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl 2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added ...Details: reservoir: 0.19M Magnesium Formate Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl 2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to coverslide in this order.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→49.061 Å / Num. obs: 186148 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.07 / Rrim(I) all: 0.187 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.96-49.0113.70.04811690.9990.020.052
2-2.0313.91.16491360.8240.4731.257

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata scaling
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→49.061 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.194 / SU B: 4.611 / SU ML: 0.125 / Average fsc free: 0.8955 / Average fsc work: 0.9103 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 9313 5.003 %Random
Rwork0.2032 176834 --
all0.205 ---
obs-186147 99.924 %-
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: 30.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.816 Å20 Å2-0 Å2
2---0.816 Å2-0 Å2
3---1.633 Å2
Refinement stepCycle: LAST / Resolution: 2.001→49.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17070 0 48 700 17818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01317449
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616291
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6423442
X-RAY DIFFRACTIONr_angle_other_deg1.3661.59237557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14452054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59723.3641082
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715153291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.74515103
X-RAY DIFFRACTIONr_chiral_restr0.0780.22113
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024117
X-RAY DIFFRACTIONr_nbd_refined0.2140.23804
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.214783
X-RAY DIFFRACTIONr_nbtor_refined0.1650.28339
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.27987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2806
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.263
X-RAY DIFFRACTIONr_nbd_other0.1870.2351
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.289
X-RAY DIFFRACTIONr_mcbond_it2.4943.18249
X-RAY DIFFRACTIONr_mcbond_other2.4913.0998247
X-RAY DIFFRACTIONr_mcangle_it3.4134.64110292
X-RAY DIFFRACTIONr_mcangle_other3.4134.64110292
X-RAY DIFFRACTIONr_scbond_it3.0913.4179199
X-RAY DIFFRACTIONr_scbond_other3.0913.4179200
X-RAY DIFFRACTIONr_scangle_it4.725.00113150
X-RAY DIFFRACTIONr_scangle_other4.725.00113151
X-RAY DIFFRACTIONr_lrange_it7.28836.13120033
X-RAY DIFFRACTIONr_lrange_other7.29436.09319871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0530.3277300.27412951X-RAY DIFFRACTION99.3898
2.053-2.1090.2926440.24912785X-RAY DIFFRACTION99.9926
2.109-2.170.2836450.24112356X-RAY DIFFRACTION99.9846
2.17-2.2370.2726320.23612023X-RAY DIFFRACTION100
2.237-2.310.2875990.23211698X-RAY DIFFRACTION99.9756
2.31-2.3910.2726290.22211258X-RAY DIFFRACTION99.9832
2.391-2.4810.2595680.2210849X-RAY DIFFRACTION99.9825
2.481-2.5830.2585540.21710438X-RAY DIFFRACTION99.9818
2.583-2.6980.2755260.22210097X-RAY DIFFRACTION100
2.698-2.8290.2715160.2139571X-RAY DIFFRACTION99.9703
2.829-2.9820.2535010.2029120X-RAY DIFFRACTION99.9688
2.982-3.1630.2624790.2148602X-RAY DIFFRACTION99.967
3.163-3.3810.2634070.2148163X-RAY DIFFRACTION99.9883
3.381-3.6520.2224100.1997564X-RAY DIFFRACTION99.9499
3.652-40.2293830.1836954X-RAY DIFFRACTION99.9455
4-4.4720.1713100.1486331X-RAY DIFFRACTION100
4.472-5.1640.2022660.1595599X-RAY DIFFRACTION99.9318
5.164-6.3230.2462600.1954723X-RAY DIFFRACTION99.9799
6.323-8.9360.1761660.1483694X-RAY DIFFRACTION99.8965
8.936-49.0610.242880.2062058X-RAY DIFFRACTION99.1682

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