[English] 日本語
Yorodumi
- PDB-8a5n: X-ray structure of human H-chain ferritin treated with SDS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a5n
TitleX-ray structure of human H-chain ferritin treated with SDS
ComponentsFerritin heavy chain
KeywordsTRANSPORT PROTEIN / ferritin / nanocage / disassembly / reassembly / sodium dodecyl sulphate
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: 1.52 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2023
Title: A new and efficient procedure to load bioactive molecules within the human heavy-chain ferritin nanocage.
Authors: Lucignano, R. / Stanzione, I. / Ferraro, G. / Di Girolamo, R. / Cane, C. / Di Somma, A. / Duilio, A. / Merlino, A. / Picone, D.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,87023
Polymers21,1241
Non-polymers74622
Water6,395355
1
AAA: Ferritin heavy chain
hetero molecules
x 24


  • defined by author&software
  • 525 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)524,879552
Polymers506,98724
Non-polymers17,892528
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area97560 Å2
ΔGint-680 kcal/mol
Surface area150560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.920, 183.920, 183.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11AAA-211-

CL

21AAA-213-

MG

31AAA-214-

MG

41AAA-222-

MG

51AAA-334-

HOH

61AAA-583-

HOH

71AAA-629-

HOH

81AAA-636-

HOH

91AAA-643-

HOH

101AAA-645-

HOH

111AAA-655-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

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


Mass: 21124.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02794, ferroxidase

-
Non-polymers , 5 types, 377 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0 M magnesium chloride 0.1 M bicine buffer pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.52→106.18 Å / Num. obs: 41266 / % possible obs: 99.5 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.016 / Rrim(I) all: 0.185 / Net I/σ(I): 41.2
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2030 / CC1/2: 0.859 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N27

5n27


Resolution: 1.52→106.18 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.091 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 2056 4.982 %
Rwork0.1513 39210 -
all0.153 --
obs-41266 99.489 %
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: 22.741 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.52→106.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 27 355 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161453
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.6392142
X-RAY DIFFRACTIONr_angle_other_deg1.6071.5923370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74123.9898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.723158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2540.2395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21201
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.213
X-RAY DIFFRACTIONr_nbd_other0.1830.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.470.261
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_mcbond_it2.2821.989752
X-RAY DIFFRACTIONr_mcbond_other2.251.982748
X-RAY DIFFRACTIONr_mcangle_it3.4612.966955
X-RAY DIFFRACTIONr_mcangle_other3.4452.964954
X-RAY DIFFRACTIONr_scbond_it3.592.322828
X-RAY DIFFRACTIONr_scbond_other3.5882.324829
X-RAY DIFFRACTIONr_scangle_it5.4483.3521183
X-RAY DIFFRACTIONr_scangle_other5.4463.3541184
X-RAY DIFFRACTIONr_lrange_it8.14127.3372015
X-RAY DIFFRACTIONr_lrange_other7.7525.6241919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5590.2271530.2162825X-RAY DIFFRACTION99.8994
1.559-1.6020.2391590.2062779X-RAY DIFFRACTION99.864
1.602-1.6490.2081520.1862691X-RAY DIFFRACTION99.7194
1.649-1.6990.2081380.1922634X-RAY DIFFRACTION99.8559
1.699-1.7550.2011300.1822548X-RAY DIFFRACTION99.7765
1.755-1.8170.2061140.1762508X-RAY DIFFRACTION99.7717
1.817-1.8850.1741230.1612355X-RAY DIFFRACTION99.12
1.885-1.9620.1861060.1562308X-RAY DIFFRACTION99.1376
1.962-2.0490.1751290.1462186X-RAY DIFFRACTION99.0586
2.049-2.1490.189930.142114X-RAY DIFFRACTION98.6148
2.149-2.2660.1721040.1312008X-RAY DIFFRACTION99.0155
2.266-2.4030.1711010.1311925X-RAY DIFFRACTION98.8293
2.403-2.5690.1591010.1321781X-RAY DIFFRACTION99.0005
2.569-2.7740.158880.1391697X-RAY DIFFRACTION99.3322
2.774-3.0390.163770.1431569X-RAY DIFFRACTION99.7576
3.039-3.3970.164830.131439X-RAY DIFFRACTION99.8033
3.397-3.9220.165550.1351288X-RAY DIFFRACTION100
3.922-4.8020.176630.1161108X-RAY DIFFRACTION100
4.802-6.7840.204500.196883X-RAY DIFFRACTION100

+
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