[English] 日本語
Yorodumi
- PDB-6j7g: Human H-ferritin mutant-C90A/C102A/C130A/D144C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j7g
TitleHuman H-ferritin mutant-C90A/C102A/C130A/D144C
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Human ferritin / Disulfide bond
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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.868 Å
AuthorsZang, J. / Chen, H. / Zhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China13730069 China
CitationJournal: Nat Commun / Year: 2019
Title: Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages.
Authors: Zang, J. / Chen, H. / Zhang, X. / Zhang, C. / Guo, J. / Du, M. / Zhao, G.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
Y: Ferritin heavy chain
Z: Ferritin heavy chain
a: Ferritin heavy chain
b: Ferritin heavy chain
e: Ferritin heavy chain
f: Ferritin heavy chain


Theoretical massNumber of molelcules
Total (without water)488,26924
Polymers488,26924
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area89470 Å2
ΔGint-300 kcal/mol
Surface area141380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.380, 165.364, 164.865
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ...
Ferritin heavy chain / / Ferritin H subunit


Mass: 20344.531 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Amonium Sulfate, HEPES

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 3.86→40.87 Å / Num. obs: 54320 / % possible obs: 92 % / Redundancy: 2.3 % / CC1/2: 0.921 / Net I/σ(I): 2.7
Reflection shellResolution: 3.86→4.9 Å / CC1/2: 0.921

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FHA

2fha


Resolution: 3.868→40.87 Å / SU ML: 0.53 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 36.01
RfactorNum. reflection% reflection
Rfree0.3279 2730 5.03 %
Rwork0.2433 --
obs0.2477 54284 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.868→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32516 0 0 8 32524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433200
X-RAY DIFFRACTIONf_angle_d1.53244737
X-RAY DIFFRACTIONf_dihedral_angle_d17.0519959
X-RAY DIFFRACTIONf_chiral_restr0.074680
X-RAY DIFFRACTIONf_plane_restr0.0075909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8682-3.93850.3921000.24951943X-RAY DIFFRACTION66
3.9385-4.01420.34931590.24872735X-RAY DIFFRACTION94
4.0142-4.09610.37181350.25982710X-RAY DIFFRACTION93
4.0961-4.18510.32051180.242537X-RAY DIFFRACTION86
4.1851-4.28240.34871370.24832528X-RAY DIFFRACTION87
4.2824-4.38950.37641460.23142724X-RAY DIFFRACTION93
4.3895-4.50810.31031480.24222764X-RAY DIFFRACTION94
4.5081-4.64060.31251550.21822682X-RAY DIFFRACTION93
4.6406-4.79030.27931440.23932776X-RAY DIFFRACTION95
4.7903-4.96140.31511160.23972845X-RAY DIFFRACTION96
4.9614-5.15980.32021380.23962792X-RAY DIFFRACTION95
5.1598-5.39440.32571270.25192881X-RAY DIFFRACTION97
5.3944-5.67840.37221760.27432885X-RAY DIFFRACTION99
5.6784-6.03360.38911710.28182845X-RAY DIFFRACTION99
6.0336-6.49860.36021260.27582922X-RAY DIFFRACTION97
6.4986-7.15080.35241850.25952815X-RAY DIFFRACTION97
7.1508-8.18170.3571440.24592627X-RAY DIFFRACTION89
8.1817-10.29310.25481870.20932664X-RAY DIFFRACTION91
10.2931-49.87590.26931180.22332879X-RAY DIFFRACTION95

+
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