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- EMDB-3434: Single-particle cryo-EM using alignment by classification (ABC):L... -

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Entry
Database: EMDB / ID: 3434
TitleSingle-particle cryo-EM using alignment by classification (ABC):Lumbricus terrestris hemoglobin at near-atomic resolution
KeywordsLumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin
SampleHemoglobin purified from Lumbricus Terrestris
SourceLumbricus terrestris / invertebrata / Common Earthworm
Map dataWorm hemoglobin cryo-EM 3D reconstruction sharpened and auto-masked
Methodsingle particle reconstruction, at 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
CitationIUCrJ, 2017, 4, 678-694

IUCrJ, 2017, 4, 678-694 Yorodumi Papers
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.
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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5m3l
  • Surface level: 1.6
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

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

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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 package.

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

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Supplemental data

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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

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Sample components

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Entire Hemoglobin purified from Lumbricus Terrestris

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

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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 / invertebrata / Common Earthworm
Source (natural)Organ or tissue: hemolymph

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Experimental details

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Sample preparation

Specimen stateparticle
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

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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)

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Image acquisition

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

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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 < Beta < 90; -30 < Gamma < +30. Anisotropic distribution of top-views and side views (see manuscript)
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 assessment)

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Atomic model buiding

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

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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