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- PDB-8oek: Crystal structure of the HormR-GAIN domains of adhesion GPCR ADGR... -

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Basic information

Entry
Database: PDB / ID: 8oek
TitleCrystal structure of the HormR-GAIN domains of adhesion GPCR ADGRB2 (BAI2) in the uncleaved state
ComponentsAdhesion G protein-coupled receptor B2
KeywordsSIGNALING PROTEIN / CIS-AUTOPROTEOLYSIS / EXTRACELLULAR / aGPCR
Function / homology
Function and homology information


calcineurin-NFAT signaling cascade / peripheral nervous system development / negative regulation of angiogenesis / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / extracellular region / membrane / plasma membrane
Similarity search - Function
: / GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. ...: / GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
CACODYLATE ION / Adhesion G protein-coupled receptor B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPohl, F. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)421152132 Germany
CitationJournal: To Be Published
Title: Structural basis of GAIN domain autoproteolysis and cleavage-resistance in the adhesion G-protein coupled receptors
Authors: Pohl, F. / Strater, N.
History
DepositionMar 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesion G protein-coupled receptor B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7443
Polymers49,3851
Non-polymers3582
Water32418
1
A: Adhesion G protein-coupled receptor B2
hetero molecules

A: Adhesion G protein-coupled receptor B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4876
Polymers98,7712
Non-polymers7164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)84.864, 95.183, 49.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1118-

HOH

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Components

#1: Protein Adhesion G protein-coupled receptor B2 / Brain-specific angiogenesis inhibitor 2


Mass: 49385.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRB2, BAI2 / Cell line (production host): HEK293S GntI- / Production host: Homo sapiens (human) / References: UniProt: O60241
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 200 mM MgCl2 and 20 % (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.77121 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77121 Å / Relative weight: 1
ReflectionResolution: 2.216→63.343 Å / Num. obs: 13145 / % possible obs: 63.8 % / Redundancy: 12.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.062 / Rrim(I) all: 0.223 / Net I/σ(I): 9.9
Reflection shellResolution: 2.216→2.447 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.855 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 658 / CC1/2: 0.567 / Rpim(I) all: 0.583 / Rrim(I) all: 1.983 / % possible all: 12.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSFeb 5, 2021 (BUILT 20210323)data reduction
Aimless0.7.7data scaling
STARANISO2.3.74 (20210424)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→63.34 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 625 4.76 %
Rwork0.2292 --
obs0.2318 13140 63.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→63.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 19 18 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032800
X-RAY DIFFRACTIONf_angle_d0.6583813
X-RAY DIFFRACTIONf_dihedral_angle_d13.5171028
X-RAY DIFFRACTIONf_chiral_restr0.042435
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.440.3262330.3211577X-RAY DIFFRACTION12
2.44-2.790.3971420.30412494X-RAY DIFFRACTION52
2.79-3.520.31972030.25224423X-RAY DIFFRACTION90
3.52-63.340.2472470.20225021X-RAY DIFFRACTION99

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