[English] 日本語
Yorodumi
- EMDB-3434: Single-particle cryo-EM using alignment by classification (ABC):L... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3434
TitleSingle-particle cryo-EM using alignment by classification (ABC):Lumbricus terrestris hemoglobin at near-atomic resolution
Map dataWorm hemoglobin cryo-EM 3D reconstruction sharpened and auto-masked
SampleHemoglobin purified from Lumbricus Terrestris:
Hemoglobin
KeywordsLumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin
Function / homologyLDL receptor-like superfamily / Globin-like superfamily / Erythrocruorin linker subunit, C-terminal superfamily / Low-density lipoprotein receptor domain class A / Annelid erythrocruorin linker subunit, C-terminal / Low-density lipoprotein (LDL) receptor class A, conserved site / Globin, extracellular / Globin/Protoglobin / Erythrocruorin / Globin ...LDL receptor-like superfamily / Globin-like superfamily / Erythrocruorin linker subunit, C-terminal superfamily / Low-density lipoprotein receptor domain class A / Annelid erythrocruorin linker subunit, C-terminal / Low-density lipoprotein (LDL) receptor class A, conserved site / Globin, extracellular / Globin/Protoglobin / Erythrocruorin / Globin / Low-density lipoprotein (LDL) receptor class A repeat / Globin / Annelid erythrocruorin linker subunit C-terminus / Globin family profile. / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Extracellular hemoglobin linker subunit, heterodimerisation domain / hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular region / metal ion binding / Extracellular globin / Extracellular globin-2 / Extracellular globin-3 / Extracellular globin-4 / Extracellular hemoglobin linker L3 subunit / Extracellular hemoglobin linker L2 subunit / Hemoglobin linker chain L1
Function and homology information
SourceLumbricus terrestris (common earthworm)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsAfanasyev P / Linnemayr-Seer C / Ravelli RBG / Matadeen R / De Carlo S / Alewijnse B / Portugal RV / Pannu NS / Schatz M / van Heel M
CitationJournal: IUCrJ / Year: 2017
Title: Single-particle cryo-EM using alignment by classification (ABC): the structure of haemoglobin.
Authors: Pavel Afanasyev / Charlotte Seer-Linnemayr / Raimond B G Ravelli / Rishi Matadeen / Sacha De Carlo / Bart Alewijnse / Rodrigo V Portugal / Navraj S Pannu / Michael Schatz / Marin van Heel
Validation ReportPDB-ID: 5m3l

SummaryFull reportAbout validation report
DateDeposition: May 11, 2016 / Header (metadata) release: Jun 15, 2016 / Map release: Jul 26, 2017 / Last update: Jul 26, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5m3l
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5m3l
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3434.map.gz (map file in CCP4 format, 182251 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.11 Å/pix.
= 399.6 Å
360 pix
1.11 Å/pix.
= 399.6 Å
360 pix
1.11 Å/pix.
= 399.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum-6.93016148 - 10
Average (Standard dev.)-4.977E-5 (0.51959878)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin-180-180-180
Limit179179179
Spacing360360360
CellA=B=C: 399.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z399.600399.600399.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-6.93010.000-0.000

-
Supplemental data

-
Mask #1

Fileemd_3434_msk.map ( map file in CCP4 format, 182251 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::
Annotation detailsAutomatic mask applied to final 3D reconstruction

-
Sample components

-
Entire Hemoglobin purified from Lumbricus Terrestris

EntireName: Hemoglobin purified from Lumbricus Terrestris / Number of components: 1 / Oligomeric State: Dodecamer
MassTheoretical: 3.6 MDa

-
Component #1: protein, Hemoglobin

ProteinName: Hemoglobin / a.k.a: Erythrocruorin / Oligomeric Details: Dodecamer / Recombinant expression: No / Number of Copies: 12
MassTheoretical: 3.6 MDa
SourceSpecies: Lumbricus terrestris (common earthworm)
Source (natural)Organ or tissue: hemolymph

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 0.1 M Tris-HCl buffer, 1 mM EDTA / pH: 7
Support filmQuantifoil grid (R2/2, Quantifoil Micro Tools GmbH)
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: 2.5 s blot time

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: May 25, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 0.02 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1200 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 5235 / Bit depth: 16

-
Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 85000 / Applied symmetry: D6 (2*6 fold dihedral) / Number of projections: 85000
Details: Reference-free Alignment By Classification (ABC-4D). Camera correction, CTF determination, particle-picking, MSA unsupervised classification, 3D reconstruction, all in IMAGIC-4D.
3D reconstructionAlgorithm: Angular reconstitution / Euler angles: Imagic D6 asymmetric triangle: 0 / Software: Imagic-4D
CTF correction: Phase flipping of micrograph patches (ctf2d-find)
Resolution: 3.8 Å / Resolution method: FSC 1/2 BIT, semi-independent
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 2GTL
Output model

+
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