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)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7RMH


Literature

Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.

Chen, M.Schmid, M.F.Chiu, W.

(2024) Nat Methods 21: 37-40

  • DOI: https://doi.org/10.1038/s41592-023-02082-9
  • Primary Citation of Related Structures:  
    8U26, 8U28, 8U2C

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. muyuanc@stanford.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short248Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1370Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]68Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35D [auth N]142Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Substance-P receptorE [auth R]418Homo sapiensMutation(s): 0 
Gene Names: TACR1NK1RTAC1R
Membrane Entity: Yes 
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Find proteins for P25103 (Homo sapiens)
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Go to UniProtKB:  P25103
PHAROS:  P25103
GTEx:  ENSG00000115353 
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UniProt GroupP25103
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  • Reference Sequence

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protachykinin-1F [auth S]11Homo sapiensMutation(s): 0 
Gene Names: TAC1NKANKNATAC2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20366 (Homo sapiens)
Explore P20366 
Go to UniProtKB:  P20366
PHAROS:  P20366
GTEx:  ENSG00000006128 
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UniProt GroupP20366
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2.99
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR21MH125285

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Structure summary