8WRZ | pdb_00008wrz

Cry-EM structure of cannabinoid receptor-beta-arrestin-1 complex

PDB DOI: https://doi.org/10.2210/pdb8WRZ/pdb
EM Map EMD-37795: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Phage display vector pTDisp, Escherichia coli
Expression System: Spodoptera frugiperda, Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-10-16 Released: 2024-02-28
Deposition Author(s): Wang, Y.X., Wang, T., Wu, L.J., Hua, T., Liu, Z.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences, National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Cryo-EM structure of cannabinoid receptor CB1-beta-arrestin complex.

Wang, Y., Wu, L., Wang, T., Liu, J., Li, F., Jiang, L., Fan, Z., Yu, Y., Chen, N., Sun, Q., Tan, Q., Hua, T., Liu, Z.J.

(2024) Protein Cell 15: 230-234

PubMed: 38102480 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/procel/pwad055
Primary Citation of Related Structures:
8WRZ

Organizational Affiliation

iHuman Institute, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content

Total Structure Weight: 129.91 kDa
Atom Count: 6,914
Modeled Residue Count: 874
Deposited Residue Count: 1,162
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-arrestin-1	A	393	Homo sapiens	Mutation(s): 0 Gene Names: ARRB1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens) Explore P49407 Go to UniProtKB: P49407
PHAROS: P49407 GTEx: ENSG00000137486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49407
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scfv30 light chain, scfv30 heavy chain	B [auth L]	268	Phage display vector pTDisp	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Cannabinoid receptor 1	C [auth R]	476	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 6 Gene Names: cybC, CNR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for P21554 (Homo sapiens) Explore P21554 Go to UniProtKB: P21554
PHAROS: P21554 GTEx: ENSG00000118432
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P21554
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vasopressin V2 receptor	D [auth V]	25	Homo sapiens	Mutation(s): 0 Gene Names: AVPR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens) Explore P30518 Go to UniProtKB: P30518
PHAROS: P30518 GTEx: ENSG00000126895
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30518
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8D0 (Subject of Investigation/LOI) Query on 8D0 Download Ideal Coordinates CCD File SDF format, chain E [auth R] MOL2 format, chain E [auth R] mmCIF format, chain E [auth R]	E [auth R]	(6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol C₂₆ H₃₉ N O₃ S JCIYJYHFBBXSBF-HMXCVIKNSA-N		Interactions Focus chain E [auth R] Interactions & Density Focus chain E [auth R]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
8D0	BindingDB: 8WRZ	Ki: 0.39 (nM) from 1 assay(s)
8D0	BindingDB: 8WRZ	EC50: 5.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91953202
Chinese Academy of Sciences	China	XDB37030104
National Science Foundation (NSF, China)	China	32022038
National Natural Science Foundation of China (NSFC)	China	31930060
National Natural Science Foundation of China (NSFC)	China	31870744

Revision History (Full details and data files)

Version 1.0: 2024-02-28
Type: Initial release
Version 1.1: 2024-03-13
Changes: Database references
Version 2.0: 2024-04-10
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-10-30
Changes: Data collection, Structure summary
Version 2.2: 2024-11-20
Changes: Data collection
Version 2.3: 2025-06-18
Changes: Data collection