[English] 日本語
Yorodumi
- PDB-6b8f: Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b8f
TitleContracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Hydrogel / Polymer
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 / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / 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 / membrane / 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 / Resolution: 1.06 Å
AuthorsZhang, L. / Bailey, J.B. / Subramanian, R. / Tezcan, F.A.
CitationJournal: Nature / Year: 2018
Title: Hyperexpandable, self-healing macromolecular crystals with integrated polymer networks.
Authors: Zhang, L. / Bailey, J.B. / Subramanian, R.H. / Tezcan, F.A.
History
DepositionOct 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,63814
Polymers21,0851
Non-polymers55313
Water6,125340
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)519,307336
Polymers506,04624
Non-polymers13,261312
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area96970 Å2
ΔGint-977 kcal/mol
Surface area138090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.040, 180.040, 180.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-63-

ARG

21A-208-

CA

31A-210-

CA

41A-211-

CA

51A-212-

CA

61A-213-

CA

71A-332-

HOH

81A-535-

HOH

91A-597-

HOH

-
Components

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


Mass: 21085.248 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 (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, ...Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, a crystal was harvested and soaked in a buffered solution comprised of 25 mM HEPES pH 7.0, 30 mM CaCl2, 8.6 % (w/v) sodium acrylate, 2.5 % (w/v) acrylamide, and 0.2 % (w/v) Bis-acrylamide overnight. Crystal was transferred to a solution containing 1 % APS and 1% TEMED with 4 M NaCl for 5 min. Crystal was then transferred to a clean slide and soaked in 30 uL H2O for 5 min. This solution was removed and the crystal was soaked in 1 M CaCl2 for 2 min. The crystal was removed, cryoprotected in perfluoro polyether, and frozen in liquid N2.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.06→63.65 Å / Num. obs: 111189 / % possible obs: 99 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4683 / CC1/2: 0.897 / % possible all: 86.4

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.06→45.01 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 6.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1026 5495 4.94 %
Rwork0.091 --
obs0.0916 111175 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 13 340 1759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131756
X-RAY DIFFRACTIONf_angle_d1.3172422
X-RAY DIFFRACTIONf_dihedral_angle_d18.762722
X-RAY DIFFRACTIONf_chiral_restr0.095255
X-RAY DIFFRACTIONf_plane_restr0.011331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.07210.17341600.17212929X-RAY DIFFRACTION84
1.0721-1.08470.1551550.14043176X-RAY DIFFRACTION90
1.0847-1.09790.13231670.12083372X-RAY DIFFRACTION96
1.0979-1.11180.13091890.1033430X-RAY DIFFRACTION99
1.1118-1.12640.11041980.09193499X-RAY DIFFRACTION99
1.1264-1.14190.10361930.0813470X-RAY DIFFRACTION100
1.1419-1.15820.07871860.07593491X-RAY DIFFRACTION100
1.1582-1.17550.09251710.07083518X-RAY DIFFRACTION100
1.1755-1.19380.07581800.0673529X-RAY DIFFRACTION100
1.1938-1.21340.08341740.0643556X-RAY DIFFRACTION100
1.2134-1.23430.07751840.06163488X-RAY DIFFRACTION100
1.2343-1.25680.07821760.06273544X-RAY DIFFRACTION100
1.2568-1.2810.07161870.06283534X-RAY DIFFRACTION100
1.281-1.30710.08171970.06483479X-RAY DIFFRACTION100
1.3071-1.33550.08741710.06873555X-RAY DIFFRACTION100
1.3355-1.36660.08442200.07013500X-RAY DIFFRACTION100
1.3666-1.40080.08091990.06843547X-RAY DIFFRACTION100
1.4008-1.43860.08681590.06753531X-RAY DIFFRACTION100
1.4386-1.4810.07411820.06753577X-RAY DIFFRACTION100
1.481-1.52880.07631720.06563539X-RAY DIFFRACTION100
1.5288-1.58340.08181810.06943582X-RAY DIFFRACTION100
1.5834-1.64680.0841740.07423574X-RAY DIFFRACTION100
1.6468-1.72180.09392010.08083554X-RAY DIFFRACTION100
1.7218-1.81260.1021960.08563571X-RAY DIFFRACTION100
1.8126-1.92610.10161880.0913601X-RAY DIFFRACTION100
1.9261-2.07480.09871720.08853602X-RAY DIFFRACTION100
2.0748-2.28360.08761650.09033655X-RAY DIFFRACTION100
2.2836-2.61410.10772000.09983645X-RAY DIFFRACTION100
2.6141-3.29330.12661920.11853697X-RAY DIFFRACTION100
3.2933-45.05060.13742060.12283935X-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