7DF9 | pdb_00007df9

Crystal of Arrestin2-V2Rpp-1-Fab30 complex

• PDB DOI: https://doi.org/10.2210/pdb7DF9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus, synthetic construct, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-06 Released: 2021-07-28 
• Deposition Author(s): Sun, J.P., Yu, X., Xiao, P., He, Q.T., Lin, J.Y., Zhu, Z.L.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2.

He, Q.T., Xiao, P., Huang, S.M., Jia, Y.L., Zhu, Z.L., Lin, J.Y., Yang, F., Tao, X.N., Zhao, R.J., Gao, F.Y., Niu, X.G., Xiao, K.H., Wang, J., Jin, C., Sun, J.P., Yu, X.

(2021) Nat Commun 12: 2396-2396

• PubMed: 33888704 
• DOI: https://doi.org/10.1038/s41467-021-22731-x
• Primary Citation of Related Structures:  
  7DF9, 7DFA, 7DFB, 7DFC


• PubMed Abstract: 
  

  Arrestins recognize different receptor phosphorylation patterns and convert this information to selective arrestin functions to expand the functional diversity of the G protein-coupled receptor (GPCR) superfamilies. However, the principles governing arrestin-phospho-receptor interactions, as well as the contribution of each single phospho-interaction to selective arrestin structural and functional states, are undefined. Here, we determined the crystal structures of arrestin2 in complex with four different phosphopeptides derived from the vasopressin receptor-2 (V2R) C-tail. A comparison of these four crystal structures with previously solved Arrestin2 structures demonstrated that a single phospho-interaction change results in measurable conformational changes at remote sites in the complex. This conformational bias introduced by specific phosphorylation patterns was further inspected by FRET and ¹ H NMR spectrum analysis facilitated via genetic code expansion. Moreover, an interdependent phospho-binding mechanism of phospho-receptor-arrestin interactions between different phospho-interaction sites was unexpectedly revealed. Taken together, our results provide evidence showing that phospho-interaction changes at different arrestin sites can elicit changes in affinity and structural states at remote sites, which correlate with selective arrestin functions.

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Organizational Affiliation: 
• Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, Jinan, Shandong, China.
Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China.
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, Jinan, Shandong, China.
Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, China.
Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, China. [e-mail].
Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, China. [e-mail].
Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, Jinan, Shandong, China. [e-mail].
Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China. [e-mail].
Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, Jinan, Shandong, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 102.85 kDa 
• Atom Count: 5,747 
• Modeled Residue Count: 800 
• Deposited Residue Count: 925 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-arrestin-1	A	426	Bos taurus	Mutation(s): 0  Gene Names: ARRB1
UniProt
Find proteins for P17870 (Bos taurus) Explore P17870  Go to UniProtKB:  P17870

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VASOPRESSIN V2 RECEPTOR PHOSPHOPEPTIDE	B [auth V]	23	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens) Explore P30518  Go to UniProtKB:  P30518
PHAROS:  P30518 GTEx:  ENSG00000126895

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB30 LIGHT CHAIN	C [auth L]	227	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB30 HEAVY CHAIN	D [auth H]	249	Mus musculus	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B [auth V]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	B [auth V]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.174	α = 90
b = 121.536	β = 90
c = 144.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Sun, J.P., Yu, X., Xiao, P., He, Q.T., Lin, J.Y., Zhu, Z.L.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary