7RMI

SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex with miniGs/q70


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Selective G protein signaling driven by substance P-neurokinin receptor dynamics.

Harris, J.A.Faust, B.Gondin, A.B.Damgen, M.A.Suomivuori, C.M.Veldhuis, N.A.Cheng, Y.Dror, R.O.Thal, D.M.Manglik, A.

(2022) Nat Chem Biol 18: 109-115

  • DOI: https://doi.org/10.1038/s41589-021-00890-8
  • Primary Citation of Related Structures:  
    7RMG, 7RMH, 7RMI

  • PubMed Abstract: 

    The neuropeptide substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via G q and G s proteins. Neurokinin A also activates NK1R, but leads to selective G q signaling. How two stimuli yield distinct G protein signaling at the same G protein-coupled receptor remains unclear. We determined cryogenic-electron microscopy structures of active NK1R bound to SP or the G q -biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent G s signaling but not G q signaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit229Homo sapiensMutation(s): 14 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Substance-P receptorB [auth R]418Homo sapiensMutation(s): 0 
Gene Names: TACR1NK1RTAC1R
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25103 (Homo sapiens)
Explore P25103 
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Substance P 6-11C [auth S]7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]370Homo 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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35F [auth N]142Lama glamaMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP5OD023048
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127359
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1138448
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1196951
Australian Research Council (ARC)AustraliaDE170100152
National Science Foundation (NSF, United States)United States2034836
Human Frontier Science Program (HFSP)United StatesLT000916/2018-L
National Institutes of Health/Office of the DirectorUnited StatesS10OD020054
National Institutes of Health/Office of the DirectorUnited StatesS10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM129541
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2022-01-05
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary