9A3K | pdb_00009a3k

Parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and arrestin 2 (5w0p-based template)

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

• PDB DOI: https://doi.org/10.2210/pdb9A3K/pdbIHM Entry Collection: PDBDEV_G_1000002

• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2023-03-24 Released: 2023-03-27 
• Deposition Author(s): Aydin, Y., Bottke, T., Lam, J.H., Ernicke, S., Fortmann, A., Tretbar, M., Zarzycka, B., Gurevich, V.V., Katritch, V., Coin, I.

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Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 1 
• Representative Model: 1 

Literature

Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells

Aydin, Y., Bottke, T., Lam, J.H., Ernicke, S., Fortmann, A., Tretbar, M., Zarzycka, B., Gurevich, V.V., Katritch, V., Coin, I.

(2023) Nat Commun 14: 1151

• PubMed: 36859440 
• DOI: https://doi.org/10.1038/s41467-023-36797-2
• Primary Citation Related Structures: 
  9A3I, 9A3J, 9A3K, 9A3L, 9A3M, 9A3N


• PubMed Abstract: 
  

  Understanding the molecular basis of arrestin-mediated regulation of GPCRs is critical for deciphering signaling mechanisms and designing functional selectivity. However, structural studies of GPCR-arrestin complexes are hampered by their highly dynamic nature. Here, we dissect the interaction of arrestin-2 (arr2) with the secretin-like parathyroid hormone 1 receptor PTH1R using genetically encoded crosslinking amino acids in live cells. We identify 136 intermolecular proximity points that guide the construction of energy-optimized molecular models for the PTH1R-arr2 complex. Our data reveal flexible receptor elements missing in existing structures, including intracellular loop 3 and the proximal C-tail, and suggest a functional role of a hitherto overlooked positively charged region at the arrestin N-edge. Unbiased MD simulations highlight the stability and dynamic nature of the complex. Our integrative approach yields structural insights into protein-protein complexes in a biologically relevant live-cell environment and provides information inaccessible to classical structural methods, while also revealing the dynamics of the system.

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Organizational Affiliation: 
• Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Bruederstr. 34, 04103, Leipzig, Germany.
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Medical Faculty, Institute for Drug Discovery, Leipzig University, Bruederstr. 34, 04103, Leipzig, Germany.
Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
Department of Phar-macology, Vanderbilt University, Nashville, TN, 37232-0146, USA.
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. [e-mail].
Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. [e-mail].
Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Bruederstr. 34, 04103, Leipzig, Germany. [e-mail].

Assembly  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Macromolecule Content 

• Total Structure Weight: 121.32 kDa 
• Atom Count: 7,142 
• Modeled Residue Count: 893 
• Deposited Residue Count: 893 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arrestin2	A	357	Homo sapiens	Mutation(s): 0  Gene Names: ARRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens) Explore P49407  Go to UniProtKB:  P49407
PHAROS:  P49407 GTEx:  ENSG00000137486

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-acting parathyroid hormone analog	B	32	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PTH1R	C [auth P]	504	Homo sapiens	Mutation(s): 0  Gene Names: PTH1R
UniProt & NIH Common Fund Data Resources
Find proteins for Q03431 (Homo sapiens) Explore Q03431  Go to UniProtKB:  Q03431
PHAROS:  Q03431 GTEx:  ENSG00000160801

Small Molecules

Non-standard Monomers  2 Unique
ID	Chains	Type	Formula	2D Diagram
SEP	C [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P
TPO	C [auth P]	L-PEPTIDE LINKING	C4 H10 N O6 P

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 1 
• Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2023-03-27 
Deposition Author(s): Aydin, Y., Bottke, T., Lam, J.H., Ernicke, S., Fortmann, A., Tretbar, M., Zarzycka, B., Gurevich, V.V., Katritch, V., Coin, I.

Revision History  

• Version 1.0: 2023-03-27
  Type: Initial release