7P02

Human Neurokinin 1 receptor (NK1R) substance P Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of neurokinin 1 receptor in complex with G q and G s proteins reveal substance P binding mode and unique activation features.

Thom, C.Ehrenmann, J.Vacca, S.Waltenspuhl, Y.Schoppe, J.Medalia, O.Pluckthun, A.

(2021) Sci Adv 7: eabk2872-eabk2872

  • DOI: https://doi.org/10.1126/sciadv.abk2872
  • Primary Citation of Related Structures:  
    7P00, 7P02

  • PubMed Abstract: 

    The neurokinin 1 receptor (NK 1 R) is involved in inflammation and pain transmission. This pathophysiologically important G protein–coupled receptor is predominantly activated by its cognate agonist substance P (SP) but also by the closely related neurokinins A and B. Here, we report cryo–electron microscopy structures of SP-bound NK 1 R in complex with its primary downstream signal mediators, G q and G s . Our structures reveal how a polar network at the extracellular, solvent-exposed receptor surface shapes the orthosteric pocket and that NK 1 R adopts a noncanonical active-state conformation with an interface for G protein binding, which is distinct from previously reported structures. Detailed comparisons with antagonist-bound NK 1 R crystal structures reveal that insurmountable antagonists induce a distinct and long-lasting receptor conformation that sterically blocks SP binding. Together, our structures provide important structural insights into ligand and G protein promiscuity, the lack of basal signaling, and agonist- and antagonist-induced conformations in the neurokinin receptor family.


  • Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody fragment scFv16A [auth H]298Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1354Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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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]71Homo 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
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortD [auth A]246Homo sapiensMutation(s): 0 
Gene Names: GNAI1GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupsP63096P63092
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Substance-P receptorE [auth R]382Homo sapiensMutation(s): 0 
Gene Names: TACR1NK1RTAC1R
Membrane Entity: Yes 
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Find proteins for P25103 (Homo sapiens)
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PHAROS:  P25103
GTEx:  ENSG00000115353 
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UniProt GroupP25103
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protachykinin-1F [auth P]12Homo sapiensMutation(s): 1 
Gene Names: TAC1NKANKNATAC2
Membrane Entity: Yes 
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Find proteins for P20366 (Homo sapiens)
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Go to UniProtKB:  P20366
PHAROS:  P20366
GTEx:  ENSG00000006128 
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UniProt GroupP20366
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182334
European Research Council (ERC)Switzerland810057-HighResCells

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release