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- PDB-8pp4: Binary crystal structure of positively supercharged ferritin vari... -

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Basic information

Entry
Database: PDB / ID: 8pp4
TitleBinary crystal structure of positively supercharged ferritin variant Ftn(pos) and reduced charge negatively supercharged ferritin variant Ftn(neg)-m3 (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 / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
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: 1.999 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, 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)257,14236
Polymers256,08412
Non-polymers1,05824
Water16,141896
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)517,97968
Polymers515,98224
Non-polymers1,99744
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 area95520 Å2
ΔGint-717 kcal/mol
Surface area146760 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)510,59176
Polymers508,35524
Non-polymers2,23652
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 area93770 Å2
ΔGint-678 kcal/mol
Surface area142240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.039, 127.039, 176.961
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-203-

CL

21L-202-

FE

31L-203-

CL

41C-317-

HOH

51C-402-

HOH

61F-388-

HOH

71J-346-

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
Details: positively supercharged human heavy chain ferritin previously published in 5JKL/5JKM/6H6T
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, N-terminally processed


Mass: 21181.443 Da / Num. of mol.: 6 / Mutation: A18E
Source method: isolated from a genetically manipulated source
Details: Human Heavy chain ferritin with 1 mutation introducing a glutamate on residue 18. Subvariant of supercharged ferritin from the previously published structure 5JKL/5JKM/6H6T
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

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Non-polymers , 4 types, 920 molecules

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


Mass: 55.845 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
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(neg)-m3 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(neg)-m3 added to coverslide in this order.
Temp details: held constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.99→49.356 Å / Num. obs: 188549 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.037 / Rrim(I) all: 0.052 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.95-49.311.90.01411660.9990.0140.02
2-2.0320.39291930.7490.3920.555

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Processing

Software
NameVersionClassification
xia2data scaling
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→49.356 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.083 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2207 9438 5.006 %
Rwork0.1814 179110 -
all0.183 --
obs-188548 99.872 %
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: 34.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.898 Å20 Å2-0 Å2
2---0.898 Å2-0 Å2
3---1.796 Å2
Refinement stepCycle: LAST / Resolution: 1.999→49.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17107 0 24 896 18027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01317660
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616461
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.64123765
X-RAY DIFFRACTIONr_angle_other_deg1.4341.59337999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88152106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96823.4031102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.932153358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7915105
X-RAY DIFFRACTIONr_chiral_restr0.0820.22140
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0220241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024177
X-RAY DIFFRACTIONr_nbd_refined0.2190.23771
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.214281
X-RAY DIFFRACTIONr_nbtor_refined0.1680.28442
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.27613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2926
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.279
X-RAY DIFFRACTIONr_nbd_other0.2060.2350
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_mcbond_it2.6983.378349
X-RAY DIFFRACTIONr_mcbond_other2.6933.3698347
X-RAY DIFFRACTIONr_mcangle_it3.6425.04110447
X-RAY DIFFRACTIONr_mcangle_other3.6395.0410447
X-RAY DIFFRACTIONr_scbond_it3.7323.7899310
X-RAY DIFFRACTIONr_scbond_other3.7323.7899311
X-RAY DIFFRACTIONr_scangle_it5.6145.52313307
X-RAY DIFFRACTIONr_scangle_other5.6145.52313308
X-RAY DIFFRACTIONr_lrange_it8.80239.18720354
X-RAY DIFFRACTIONr_lrange_other8.81239.04920127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0510.2886950.25613138X-RAY DIFFRACTION99.3322
2.051-2.1070.2726590.23212907X-RAY DIFFRACTION99.9779
2.107-2.1680.2666680.2112527X-RAY DIFFRACTION99.9773
2.168-2.2350.2746190.21412211X-RAY DIFFRACTION99.9922
2.235-2.3080.255790.19411895X-RAY DIFFRACTION99.984
2.308-2.3890.2366710.18811329X-RAY DIFFRACTION99.9084
2.389-2.480.2425910.19511024X-RAY DIFFRACTION99.8281
2.48-2.5810.255630.18910561X-RAY DIFFRACTION99.982
2.581-2.6950.244710.19210259X-RAY DIFFRACTION99.9721
2.695-2.8270.245270.1849722X-RAY DIFFRACTION99.9707
2.827-2.980.2145030.1789246X-RAY DIFFRACTION99.9897
2.98-3.1610.2254630.1998809X-RAY DIFFRACTION99.9784
3.161-3.3790.2584290.2028196X-RAY DIFFRACTION99.9073
3.379-3.6490.2493670.1927708X-RAY DIFFRACTION99.6914
3.649-3.9970.1883870.1637060X-RAY DIFFRACTION99.9597
3.997-4.4690.1673790.1346334X-RAY DIFFRACTION99.9702
4.469-5.160.1672870.1295671X-RAY DIFFRACTION99.8827
5.16-6.3180.2092610.174778X-RAY DIFFRACTION99.9207
6.318-8.930.1741980.1473699X-RAY DIFFRACTION99.7951
8-49.310.1761210.2172036X-RAY DIFFRACTION98.1793

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