[English] 日本語
Yorodumi
- PDB-8pp4: Binary crystal structure of positively supercharged ferritin vari... -

+
Open data


ID or keywords:

Loading...

-
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 / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / 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 / 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: 1.999 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

-
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, 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

-
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
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

-
Non-polymers , 4 types, 920 molecules

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


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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.79 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

-
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

-
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

+
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