[English] 日本語
Yorodumi
- EMDB-2825: Cryo-EM structure of worm hemoglobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2825
TitleCryo-EM structure of worm hemoglobin
Map dataLumbricus terrestris
Sample
  • Sample: Worm Hemoglobin
  • Protein or peptide: Hemoglobin
KeywordsLombricus / hemoglobin / heme
Biological speciesLumbricus terrestris (common earthworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsDe Carlo S / Matadeen R / van Heel M
CitationJournal: To Be Published
Title: Cryo-EM structure of worm hemoglobin
Authors: De Carlo S
History
DepositionNov 23, 2014-
Header (metadata) releaseDec 10, 2014-
Map releaseDec 10, 2014-
UpdateMar 11, 2015-
Current statusMar 11, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2825.jpg

Downloads & links

-
Map

FileDownload / File: emd_2825.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLumbricus terrestris
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.69406313 - 0.76194
Average (Standard dev.)-0.00087601 (±0.0847344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-126-126-126
Dimensions256256256
Spacing256256256
CellA=B=C: 350.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-126-126-126
NC/NR/NS256256256
D min/max/mean-0.6940.762-0.001

-
Supplemental data

-
Sample components

-
Entire : Worm Hemoglobin

EntireName: Worm Hemoglobin
Components
  • Sample: Worm Hemoglobin
  • Protein or peptide: Hemoglobin

-
Supramolecule #1000: Worm Hemoglobin

SupramoleculeName: Worm Hemoglobin / type: sample / ID: 1000 / Oligomeric state: One homo-dodecamer / Number unique components: 1
Molecular weightExperimental: 3.5 MDa / Theoretical: 3.5 MDa

-
Macromolecule #1: Hemoglobin

MacromoleculeName: Hemoglobin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Dodecamer / Recombinant expression: No
Source (natural)Organism: Lumbricus terrestris (common earthworm) / synonym: Earth Worm
Molecular weightExperimental: 3.5 MDa / Theoretical: 3.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Zemlin Tableau
DetailsParallel Illumination, NanoProbe
DateJun 22, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: IMAGIC, 4D / Number images used: 40000

+
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