8OEK | pdb_00008oek

Crystal structure of the HormR-GAIN domains of adhesion GPCR ADGRB2 (BAI2) in the uncleaved state

PDB DOI: https://doi.org/10.2210/pdb8OEK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-03-10 Released: 2023-05-31
Deposition Author(s): Pohl, F., Strater, N.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.287 (Depositor), 0.290 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of GAIN domain autoproteolysis and cleavage-resistance in the adhesion G-protein coupled receptors

Pohl, F., Strater, N.

To be published.

Macromolecule Content

Total Structure Weight: 49.74 kDa
Atom Count: 2,754
Modeled Residue Count: 344
Deposited Residue Count: 449
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesion G protein-coupled receptor B2	A	449	Homo sapiens	Mutation(s): 0 Gene Names: ADGRB2, BAI2
UniProt & NIH Common Fund Data Resources
Find proteins for O60241 (Homo sapiens) Explore O60241 Go to UniProtKB: O60241
PHAROS: O60241 GTEx: ENSG00000121753
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60241
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: O60241-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.287 (Depositor), 0.290 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.864	α = 90
b = 95.183	β = 90
c = 49.465	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	421152132

Revision History (Full details and data files)

Version 1.0: 2023-05-31
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.