9VB6 | pdb_00009vb6

Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the GTP-bound, AHD-open C state, plunge-frozen 8 seconds after GTP addition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9VB6

This is version 1.0 of the entry. See complete history

Literature

The dynamic basis of G-protein recognition and activation by a GPCR.

Kobayashi, K.Kawakami, K.Matsui, T.E.Yokoi, S.Fukuda, M.Narita, T.J.Arai, H.Tambo, M.Sumikama, T.Tatsumi, M.Yamashita, K.Koyanagi, J.Kugawa, M.Ikeda, H.Sumino, A.Mitsutake, A.Kobilka, B.K.Inoue, A.Kato, H.E.

(2026) Nature 652: 812-821

  • DOI: https://doi.org/10.1038/s41586-026-10228-w
  • Primary Citation Related Structures: 
    20ZC, 20ZD, 20ZG, 20ZH, 20ZI, 20ZJ, 20ZK, 20ZL, 9VAT, 9VAU, 9VAV, 9VAW, 9VAX, 9VAY, 9VAZ, 9VB0, 9VB1, 9VB2, 9VB3, 9VB4, 9VB5, 9VB6, 9VB7, 9VBA

  • PubMed Abstract: 

    G-protein-coupled receptor (GPCR) signalling occurs through heterotrimeric G proteins, whose selective activation leads to distinct cellular outcomes 1 . Although more than 200 GPCR-G protein complex structures have been determined 2 , these static snapshots provide limited insight into the dynamics of G-protein association and dissociation. Here we present cryo-electron microscopy structures of human neurotensin receptor type 1 (NTSR1) with minimally modified G o and G q , showing how the receptor's intracellular surface dynamically rearranges to accommodate each G-protein subtype. Furthermore, time-resolved cryo-electron microscopy analyses of NTSR1-G i visualized G-protein dissociation processes on GDP/GTP binding. Characterization of more than 20 intermediates, complemented by mutational and computational analyses, identifies four key mechanistic features. First, GDP/GTP induces G i release from both canonical and non-canonical active conformations with distinct kinetics. Second, NTSR1 uses common intracellular rearrangements to recognize different G-protein subtypes and to promote activation of a single subtype. Third, separation from Gβγ involves stepwise remodelling of the Gα switches I-III. Finally, G i dissociates from the receptor through a pathway that is distinct from that of G s , and the canonical and non-canonical NTSR1-G i complexes further diverge in their dissociation trajectories. These findings provide a comprehensive framework for understanding GPCR signalling dynamics and guiding signal-targeted therapeutic development.


  • Organizational Affiliation
    • Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Japan.

Macromolecule Content 

  • Total Structure Weight: 165.3 kDa 
  • Atom Count: 9,129 
  • Modeled Residue Count: 1,177 
  • Deposited Residue Count: 1,484 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1358Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62873
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59768
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16259Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurotensin receptor type 1E [auth R]436Homo sapiensMutation(s): 1 
Gene Names: NTSR1NTRR
UniProt & NIH Common Fund Data Resources
Find proteins for P30989 (Homo sapiens)
Explore P30989 
Go to UniProtKB:  P30989
PHAROS:  P30989
GTEx:  ENSG00000101188 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30989
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
JMV449F [auth L]6synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
G [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan25K09525
Japan Society for the Promotion of Science (JSPS)Japan24H02262
Japan Society for the Promotion of Science (JSPS)Japan25H01338
Japan Society for the Promotion of Science (JSPS)Japan24KJ0981
Japan Society for the Promotion of Science (JSPS)Japan25H02243
Japan Society for the Promotion of Science (JSPS)Japan24K18060
Japan Society for the Promotion of Science (JSPS)Japan23KJ0363

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release