[English] 日本語
Yorodumi
- PDB-8pp3: Binary crystal structure of positively supercharged ferritin vari... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 1.55 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 994 molecules

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


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


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


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more