6J21 | pdb_00006j21

Crystal structure of the human NK1 substance P receptor

• PDB DOI: https://doi.org/10.2210/pdb6J21/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-12-30 Released: 2019-03-06 
• Deposition Author(s): Chen, S., Lu, M., Zhang, H., Wu, B., Zhao, Q.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography.

Chen, S., Lu, M., Liu, D., Yang, L., Yi, C., Ma, L., Zhang, H., Liu, Q., Frimurer, T.M., Wang, M.W., Schwartz, T.W., Stevens, R.C., Wu, B., Wuthrich, K., Zhao, Q.

(2019) Nat Commun 10: 638-638

• PubMed: 30733446 
• DOI: https://doi.org/10.1038/s41467-019-08568-5
• Primary Citation of Related Structures:  
  6J20, 6J21


• PubMed Abstract: 
  

  Neurokinin 1 receptor (NK1R) has key regulating functions in the central and peripheral nervous systems, and NK1R antagonists such as aprepitant have been approved for treating chemotherapy-induced nausea and vomiting. However, the lack of data on NK1R structure and biochemistry has limited further drug development targeting this receptor. Here, we combine NMR spectroscopy and X-ray crystallography to provide dynamic and static characterisation of the binding mode of aprepitant in complexes with human NK1R variants. ¹⁹ F-NMR showed a slow off-rate in the binding site, where aprepitant occupies multiple substates that exchange with frequencies in the millisecond range. The environment of the bound ligand is affected by the amino acid in position 2.50, which plays a key role in ligand binding and receptor signaling in class A GPCRs. Crystal structures now reveal how receptor signaling relates to the conformation of the conserved NP ^7.50 xxY motif in transmembrane helix VII.

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Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.
CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China.
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Pudong, Shanghai, 201203, China.
Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen, 2200, Denmark.
School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China.
CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. [e-mail].
CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China. [e-mail].
CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. [e-mail].
CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.32 kDa 
• Atom Count: 3,138 
• Modeled Residue Count: 398 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Substance-P receptor,Endolysin	A	441	Homo sapiens, Tequatrovirus T4	Mutation(s): 5  Gene Names: TACR1, NK1R, TAC1R, e, T4Tp126 EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P25103 (Homo sapiens) Explore P25103  Go to UniProtKB:  P25103
PHAROS:  P25103 GTEx:  ENSG00000115353
UniProt Groups	P00720P25103

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GBQ	B [auth A]	5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one C23 H21 F7 N4 O3 ATALOFNDEOCMKK-OITMNORJSA-N
OLC	C [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.256 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.11	α = 90
b = 103.11	β = 90
c = 158.16	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Chen, S., Lu, M., Zhang, H., Wu, B., Zhao, Q.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	QYZDB-SSW-SMC054

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary