[English] 日本語
Yorodumi
- EMDB-3854: Cryo-EM structure of human apoferritin at 3.15 A resolution deter... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3854
TitleCryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate
Map dataCryo-EM structure of human apoferritin at 3.15 A determined with the Volta phase plate
Samplehuman h-ferritin:
Function / homologyFerritin iron-binding regions signature 2. / Ferritin-like / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain / Ferritin-like superfamily / Ferritin, conserved site / Scavenging by Class A Receptors ...Ferritin iron-binding regions signature 2. / Ferritin-like / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain / Ferritin-like superfamily / Ferritin, conserved site / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / Neutrophil degranulation / Iron uptake and transport / Ferritin-like domain / negative regulation of necrotic cell death / go:0097286: / intracellular ferritin complex / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / cellular iron ion homeostasis / tertiary granule lumen / 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 / Ferritin heavy chain
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.15 Å resolution
AuthorsPechnikova EV
CitationJournal: To Be Published
Title: Cryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate
Authors: Pechnikova EV
DateDeposition: Aug 25, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 8, 2017

-
Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3854.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.50788814 - 0.61861026
Average (Standard dev.)0.0023143764 (0.05956288)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 164.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z164.000164.000164.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.5080.6190.002

-
Supplemental data

-
Sample components

-
Entire human h-ferritin

EntireName: human h-ferritin
Details: The sample was prepared in National Laboratory of Biomacromolecules, IBP, China
Number of components: 2

-
Component #1: protein, human h-ferritin

ProteinName: human h-ferritin
Details: The sample was prepared in National Laboratory of Biomacromolecules, IBP, China
Recombinant expression: No
MassTheoretical: 509 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #2: protein, human h-ferritin

ProteinName: human h-ferritin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: PBS / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 58 e/Å2 / Illumination mode: OTHER
LensMagnification: 96000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: OTHER
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 8396
3D reconstructionSoftware: RELION / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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