[English] 日本語
Yorodumi
- PDB-8b7l: X-ray structure of Auranofin-horse spleen ferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b7l
TitleX-ray structure of Auranofin-horse spleen ferritin
ComponentsFerritin light chain
KeywordsTRANSPORT PROTEIN / ferritin / gold / encapsulation / auranofin / anticancer
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / 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 light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsFerraro, G. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2022
Title: Evaluation of Auranofin Loading within Ferritin Nanocages.
Authors: Lucignano, R. / Pratesi, A. / Imbimbo, P. / Monti, D.M. / Picone, D. / Messori, L. / Ferraro, G. / Merlino, A.
History
DepositionSep 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,28415
Polymers19,8721
Non-polymers1,41114
Water6,071337
1
AAA: Ferritin light chain
hetero molecules

AAA: Ferritin light chain
hetero molecules

AAA: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,85145
Polymers59,6173
Non-polymers4,23342
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_753z+2,x,y-21
crystal symmetry operation9_573y,z+2,x-21
Unit cell
Length a, b, c (Å)181.990, 181.990, 181.990
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-204-

CD

21AAA-205-

CD

31AAA-208-

CD

41AAA-214-

CL

51AAA-516-

HOH

61AAA-527-

HOH

71AAA-557-

HOH

81AAA-609-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

-
Non-polymers , 5 types, 351 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#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.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.8 M ammonium sulphate 0.1 M TrisHCl pH 7.4 60 mM cadmium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→64.34 Å / Num. obs: 88885 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.014 / Net I/σ(I): 34.9
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 15 % / Rmerge(I) obs: 1.8 / Num. unique obs: 3593 / CC1/2: 0.772 / Rpim(I) all: 0.364 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERK

5erk


Resolution: 1.24→64.34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.5 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1798 4449 5.005 %
Rwork0.1582 84436 -
all0.159 --
obs-88885 98.147 %
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: 15.916 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.24→64.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 27 337 1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171520
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1980.017
X-RAY DIFFRACTIONr_angle_refined_deg2.2431.6362258
X-RAY DIFFRACTIONr_angle_other_deg1.661.5833545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16421.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0221516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02380
X-RAY DIFFRACTIONr_nbd_refined0.2920.2443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21295
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2785
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3410.231
X-RAY DIFFRACTIONr_nbd_other0.2460.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3250.266
X-RAY DIFFRACTIONr_mcbond_it1.8991.27806
X-RAY DIFFRACTIONr_mcbond_other1.8011.266805
X-RAY DIFFRACTIONr_mcangle_it2.371.8941044
X-RAY DIFFRACTIONr_mcangle_other2.3691.8981045
X-RAY DIFFRACTIONr_scbond_it3.1061.601843
X-RAY DIFFRACTIONr_scbond_other3.0951.602840
X-RAY DIFFRACTIONr_scangle_it4.6722.2821211
X-RAY DIFFRACTIONr_scangle_other4.6812.2791205
X-RAY DIFFRACTIONr_lrange_it7.88519.3492136
X-RAY DIFFRACTIONr_lrange_other7.27517.3142010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.251-1.2890.2633080.2395765X-RAY DIFFRACTION100
1.331-1.3780.2052670.1985467X-RAY DIFFRACTION100
1.378-1.430.1982510.1825287X-RAY DIFFRACTION100
1.488-1.5550.1712490.1464888X-RAY DIFFRACTION100
1.555-1.630.1512670.1334628X-RAY DIFFRACTION100
1.63-1.7190.1432340.1264440X-RAY DIFFRACTION100
1.719-1.8230.162090.1274213X-RAY DIFFRACTION99.9774
1.823-1.9490.1672200.1333965X-RAY DIFFRACTION100
1.949-2.1050.1581830.143699X-RAY DIFFRACTION100
2.105-2.3060.1621960.1273424X-RAY DIFFRACTION100
2.306-2.5780.1651650.1323128X-RAY DIFFRACTION100
2.578-2.9760.1771680.1342756X-RAY DIFFRACTION100
2.976-3.6440.1691370.1362382X-RAY DIFFRACTION100
3.644-5.150.1681060.1451895X-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