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2019 Model Metrics Challenge

Goals

Identify metrics most suitable for evaluating and comparing fit of atomic coordinate models into cryo-EM maps for specimens in the 1.5-4.0 Å reported overall resolution range.

Specific metrics for review:

  1. Model geometry and rotamer configuration
  2. Overall fit of model into map density per residue and per atom
  3. Domain or secondary-structure element fit
  4. Resolvability at residue or atom-level
  5. Atomic Displacement parameters (B-factors) recommended optimization practice

Targets

There are two target specimens for this challenge. 

  • Human Heavy-chain Apoferritin: a series of three maps is provided (#1 - #3), which differ only in the number of particles used for reconstruction.  These maps were chosen so that different metrics can be carefully compared/contrasted at different resolutions.
  • Horse Liver Alcohol Dehydrogenase: one map is provided (#4). This structure has the extra challenge of fitting a ligand as well as the protein chain.

Target Map Download: You can use this rsync script. Alternatively, you can download individual maps from EMDB atlas pages (click on EMDB entry link in the table below, select "download" tab).

  1. Human Apoferritin
2. Human Apoferritin
3. Human Apoferritin
4. Horse Liver Alcohol Dehydrogenase

target

apoferritin apoferritin apoferritin
EMDB entry
Reported Resolution (Å)

EMD-20026
1.8

EMD-20027
2.3
EMD-20028
3.1
EMD-0406
2.9
Sharpened/Masked map emd_20026.map emd_20027.map emd_20028.map emd_0406.map
Unsharpened/Unmasked map emd_20026_additional_2.map emd_20027_additional_1.map emd_20028_additional_1.map
emd_0406_additional.map
Single protomer map emd_20026_additional_1.map emd_20027_additional_2.map emd_20028_additional_2.map

n/a

Half-maps emd_20026_half_map_1.map, emd_20026_half_map_2.map emd_20027_half_map_1.map, emd_20027_half_map_1.map emd_20028_half_map_1.map,
emd_20028_half_map_2.map
emd_0406_half_map_1.map,
emd_0406_half_map_2.map
Primary Citation

unpublished

Herzik et al, 2019
Reference Models

   2fha (Xray)

3ajo (Xray)

6nbb (EM)

2jhf (Xray)

Imposed Map Symmetry

Octahedral (O)

 Cyclic (C2)
 Specimen MW
21 kDa x 24-fold = 504 kDa  40 kDa x 2-fold = 80 kDa
Map Contributors

 Kaiming Zhang, Greg Pintilie, Shanshan Li, Wah Chiu

Mark Herzik, Mengyu Wu, Gabe Lander

 

Modelling Instructions

  • Ab initio modelling is encouraged but not required.
  • Regardless of the modelling method used, submitted models should be as complete and as accurate as possible (i.e., close to publication-ready).
  • For the apoferritin targets, use a separate modelling processes for each (do not "cross" datasets).
  • Fitting to either the unsharpened/unmasked map or one of the half-maps is strongly encouraged.
  • Submission in mmCIF format is strongly encouraged.

Human heavy chain Apoferritin (#1-3)

Deposit: Single subunit, chain A, with position given by single protomer map

Chain residue numbering starts with 1

Symmetry Matrices (center at x=y=z=109.2 Angstroms)

Full Sequence (Uniprot P02794)

TTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRI
FLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGA
PESGLAEYLFDKHTLGDSDNES

Horse liver Alcohol Dehydrogenase (#4)

Deposit: either single subunit (Chain A) or Dimer (chains A and B). Chain positions same as 6nbb

Chain residue numbering starts with 1

For associated ligand NAD, use same chain id as protein, residue#=401

Symmetry Matrices (2-fold at x=y=142.976 Angstroms)

Full Sequence (Uniprot P00327)

STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGV
TTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKI
DAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATEC
VNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFG
GFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF

 

Process

  1. Participant Teleconference to review process, gather recommendations for deposition data collection and automated model comparison pipeline.
  2. Participants prepare/upload their best models for each target (team approach to modelling is welcome). 
  3. Initial (blinded) analyses of deposited models will be performed via the automated model comparison pipeline (guided by recommendations in step #1).
  4. Participant Panel will meet to review the results at June Face-to-Face meeting and recommend next steps.

 

Timeline

17 April  Open Challenge
19-29 April Participant Teleconference(s)
 1 May  Deposition form opens to collect participant models
 25 May  Deadline for depositing models
 6 June  Results of model-compare pipeline made available
 13-15 June  Participant Face-to-Face Meeting

EMDataResource Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdataresource.org

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