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Title: Measurement of atom resolvability in cryo-EM maps with Q-scores

Abstract

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]
+ Show Author Affiliations
  1. Stanford Univ., CA (United States)
  2. SLAC National Accelerator Lab., Stanford Univ., Menlo Park, CA (United States)
  3. Stanford Univ., CA (United States); SLAC National Accelerator Lab., Stanford Univ., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Inst. of Health
OSTI Identifier:
1604578
Grant/Contract Number:  
AC02-76SF00515; R01GM079429; P41GM103832; S10OD021600
Resource Type:
Accepted Manuscript
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 17; Journal Issue: 3; Journal ID: ISSN 1548-7091
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., and Chiu, Wah. Measurement of atom resolvability in cryo-EM maps with Q-scores. United States: N. p., 2020. Web. doi:10.1038/s41592-020-0731-1.
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Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., & Chiu, Wah. Measurement of atom resolvability in cryo-EM maps with Q-scores. United States. https://doi.org/10.1038/s41592-020-0731-1
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Pintilie, Grigore, Zhang, Kaiming, Su, Zhaoming, Li, Shanshan, Schmid, Michael F., and Chiu, Wah. Mon . "Measurement of atom resolvability in cryo-EM maps with Q-scores". United States. https://doi.org/10.1038/s41592-020-0731-1. https://www.osti.gov/servlets/purl/1604578.
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@article{osti_1604578,
title = {Measurement of atom resolvability in cryo-EM maps with Q-scores},
author = {Pintilie, Grigore and Zhang, Kaiming and Su, Zhaoming and Li, Shanshan and Schmid, Michael F. and Chiu, Wah},
abstractNote = {Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.},
doi = {10.1038/s41592-020-0731-1},
journal = {Nature Methods},
number = 3,
volume = 17,
place = {United States},
year = {Mon Feb 10 00:00:00 EST 2020},
month = {Mon Feb 10 00:00:00 EST 2020}
}
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https://doi.org/10.1038/s41592-020-0731-1
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Works referenced in this record:

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
journal, July 2016

New software tools in EMAN2 inspired by EMDatabank map challenge
journal, November 2018

  • Bell, James M.; Chen, Muyuan; Durmaz, Tunay
  • Journal of Structural Biology, Vol. 204, Issue 2
  • DOI: 10.1016/j.jsb.2018.09.002

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy
journal, July 2017

  • Joseph, Agnel Praveen; Lagerstedt, Ingvar; Patwardhan, Ardan
  • Journal of Structural Biology, Vol. 199, Issue 1
  • DOI: 10.1016/j.jsb.2017.05.007

Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment
journal, May 2016

Atomic Dispacement Parameter Nomenclature. Report of a Subcommittee on Atomic Displacement Parameter Nomenclature
journal, September 1996

  • Trueblood, K. N.; Bürgi, H. B.; Burzlaff, H.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 52, Issue 5
  • DOI: 10.1107/S0108767396005697

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures
journal, October 2017

  • Meyder, Agnes; Nittinger, Eva; Lange, Gudrun
  • Journal of Chemical Information and Modeling, Vol. 57, Issue 10
  • DOI: 10.1021/acs.jcim.7b00391

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Applications of the molecular dynamics flexible fitting method
journal, March 2011

  • Trabuco, Leonardo G.; Schreiner, Eduard; Gumbart, James
  • Journal of Structural Biology, Vol. 173, Issue 3
  • DOI: 10.1016/j.jsb.2010.09.024

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
journal, August 2015

  • Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3541

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

  • Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
  • DOI: 10.1073/pnas.1621152114

Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen
journal, August 2020

  • Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6
  • DOI: 10.1007/s00775-020-01814-y

Cryo-EM model validation using independent map reconstructions: Cryo-EM Model Validation
journal, May 2013

  • DiMaio, Frank; Zhang, Junjie; Chiu, Wah
  • Protein Science, Vol. 22, Issue 6
  • DOI: 10.1002/pro.2267

Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
journal, October 2009

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
journal, September 2009

  • DiMaio, Frank; Tyka, Michael D.; Baker, Matthew L.
  • Journal of Molecular Biology, Vol. 392, Issue 1
  • DOI: 10.1016/j.jmb.2009.07.008

How large B-factors can be in protein crystal structures
journal, February 2018

Water Networks Can Determine the Affinity of Ligand Binding to Proteins
journal, September 2019

  • Darby, John F.; Hopkins, Adam P.; Shimizu, Seishi
  • Journal of the American Chemical Society, Vol. 141, Issue 40
  • DOI: 10.1021/jacs.9b06275

New tools for automated high-resolution cryo-EM structure determination in RELION-3
journal, November 2018

  • Zivanov, Jasenko; Nakane, Takanori; Forsberg, Björn O.
  • eLife, Vol. 7
  • DOI: 10.7554/eLife.42166

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage
journal, February 2016

  • Pintilie, Grigore; Chen, Dong-Hua; Haase-Pettingell, Cameron A.
  • Biophysical Journal, Vol. 110, Issue 4
  • DOI: 10.1016/j.bpj.2015.11.3522

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017

  • Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul
  • Nature Methods, Vol. 14, Issue 4
  • DOI: 10.1038/nmeth.4193

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318006551

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores
journal, December 2018

Quantifying the local resolution of cryo-EM density maps
journal, November 2013

  • Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D.
  • Nature Methods, Vol. 11, Issue 1
  • DOI: 10.1038/nmeth.2727

A beginner's guide to radiation damage
journal, February 2009

Interpretation of atomic displacement parameters from diffraction studies of crystals
journal, February 1988

  • Dunitz, Jack D.; Schomaker, Verner; Trueblood, Kenneth N.
  • The Journal of Physical Chemistry, Vol. 92, Issue 4
  • DOI: 10.1021/j100315a002
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    Works referencing / citing this record:

    Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution
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    Structural basis for strand-transfer inhibitor binding to HIV intasomes
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