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Yorodumi- PDB-5m3l: Single-particle cryo-EM using alignment by classification (ABC): ... -
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-Basic information
Entry | Database: PDB / ID: 5m3l | |||||||||||||||||||||
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Title | Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin | |||||||||||||||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Lumbricus terrestris / hemoglobin / oxygen carrier / erythrocruorin | |||||||||||||||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Lumbricus terrestris (common earthworm) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||
Authors | Afanasyev, P. / Linnemayr-Seer, C. / Ravelli, R.B.G. / Matadeen, R. / De Carlo, S. / Alewijnse, B. / Portugal, R.V. / Pannu, N.S. / Schatz, M. / van Heel, M. | |||||||||||||||||||||
Funding support | Netherlands, United Kingdom, Brazil, 6items
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Citation | Journal: 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 / Abstract: Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in ...Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5m3l.cif.gz | 490.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3l.ent.gz | 395.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m3l_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5m3l_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5m3l_validation.xml.gz | 83.4 KB | Display | |
Data in CIF | 5m3l_validation.cif.gz | 116.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3l ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3l | HTTPS FTP |
-Related structure data
Related structure data | 3434MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: D6 (2x6 fold dihedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
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