7RMH

Substance P bound to active human neurokinin 1 receptor in complex with miniGs399


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8U26


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 short248Homo sapiensMutation(s): 6 
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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  • Reference Sequence
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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
Substance PF [auth S]12Homo sapiensMutation(s): 1 
Membrane Entity: Yes 
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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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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary