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TitleImproving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.
Journal, issue, pagesNat Methods, Vol. 21, Issue 1, Page 37-40, Year 2024
Publish dateNov 16, 2023
AuthorsMuyuan Chen / Michael F Schmid / Wah Chiu /
PubMed AbstractCryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian ...Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.
External linksNat Methods / PubMed:37973972 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.1 Å
Structure data

41840

8u26

EMDB-41840, PDB-8u26:
Gaussian Mixture Models based single particle refinement - GPCR (Substance P bound to active human neurokinin 1 receptor in complex with miniGs399 from EMPIAR-10786)
Method: EM (single particle) / Resolution: 2.5 Å

41841

8u28

EMDB-41841, PDB-8u28:
Gaussian mixture model based single particle refinement - SARS (SARS-CoV-2 Spike Proteins on intact virions from EMPIAR-10492)
Method: EM (single particle) / Resolution: 3.1 Å

41845

8u2c

EMDB-41845, PDB-8u2c:
Gaussian mixture model based single particle refinement - ABC transporter (inhibitor-bound ABCG2 from EMPIAR-10374)
Method: EM (single particle) / Resolution: 2.5 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • homo sapiens (human)
  • lama glama (llama)
  • severe acute respiratory syndrome coronavirus 2
  • mus musculus (house mouse)
KeywordsMEMBRANE PROTEIN / GPCR / VIRUS / coronavirus spike protein / ABC transporter

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