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- PDB-8hc0: Crystal structure of the extracellular domains of GPR110 -

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Basic information

Entry
Database: PDB / ID: 8hc0
TitleCrystal structure of the extracellular domains of GPR110
Components(Adhesion G-protein coupled receptor ...) x 3
KeywordsCELL ADHESION / Adhesion GPCR / GPR110 / synaptamide / molecular dynamics simulations
Function / homology
Function and homology information


energy reserve metabolic process / fat cell differentiation / regulation of lipid metabolic process / synapse assembly / G protein-coupled receptor activity / memory / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron projection development / cytoplasmic vesicle / cell surface receptor signaling pathway ...energy reserve metabolic process / fat cell differentiation / regulation of lipid metabolic process / synapse assembly / G protein-coupled receptor activity / memory / adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuron projection development / cytoplasmic vesicle / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / extracellular region / membrane / plasma membrane
Similarity search - Function
GPCR family 2, Ig-hepta-like receptor / : / SEA domain profile. / SEA domain / SEA domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. ...GPCR family 2, Ig-hepta-like receptor / : / SEA domain profile. / SEA domain / SEA domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / 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
Adhesion G-protein coupled receptor F1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, F.F. / Song, G.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171215 China
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Crystal Structure of the Extracellular Domains of GPR110.
Authors: Wang, F. / Wang, Y. / Qiu, W. / Zhang, Q. / Yang, H. / Song, G.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 30, 2024Group: Structure summary / Category: 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 F1
C: Adhesion G-protein coupled receptor F1
B: Adhesion G-protein coupled receptor F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14711
Polymers48,5263
Non-polymers2,6218
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint1 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.825, 47.993, 87.023
Angle α, β, γ (deg.)90.00, 127.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Adhesion G-protein coupled receptor ... , 3 types, 3 molecules ACB

#1: Protein Adhesion G-protein coupled receptor F1 / G protein-coupled receptor 110 / G protein-coupled receptor KPG_012 / G protein-coupled receptor PGR19


Mass: 39499.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRF1, GPR110, PGR19 / Cell line (production host): HEK293gnt-
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: Q5T601
#2: Protein/peptide Adhesion G-protein coupled receptor F1 / G protein-coupled receptor 110 / G protein-coupled receptor KPG_012 / G protein-coupled receptor PGR19


Mass: 2413.712 Da / Num. of mol.: 1 / Fragment: C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRF1, GPR110, PGR19 / Cell line (production host): HEK293gnt-
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: Q5T601
#3: Protein Adhesion G-protein coupled receptor F1 / G protein-coupled receptor 110 / G protein-coupled receptor KPG_012 / G protein-coupled receptor PGR19


Mass: 6612.419 Da / Num. of mol.: 1 / Fragment: N-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRF1, GPR110, PGR19 / Cell line (production host): HEK293gnt-
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: Q5T601

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Sugars , 2 types, 8 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 1 types, 45 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG-MME 2,000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→43.8 Å / Num. obs: 18390 / % possible obs: 98 % / Redundancy: 3.18 % / CC1/2: 0.989 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.149 / Net I/σ(I): 9.68
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.9-3.070.57915550.7320.7011
3.07-3.280.41615110.8620.4951
3.28-3.540.27414010.920.3271
3.54-3.880.18212720.970.2181
3.88-4.330.11911990.980.1431
4.33-50.08310150.9870.11
5-6.10.0838820.9880.1011
6.1-8.540.0626890.9930.0761
8.54-43.80.0494090.9950.061

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Processing

Software
NameVersionClassification
PHENIXphenix-1.19.2-4158refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted by AlphaFold2

Resolution: 2.9→19.8 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 938 5.1 %
Rwork0.2325 --
obs0.2355 18390 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 42 45 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053544
X-RAY DIFFRACTIONf_angle_d0.5794819
X-RAY DIFFRACTIONf_dihedral_angle_d10.303545
X-RAY DIFFRACTIONf_chiral_restr0.156605
X-RAY DIFFRACTIONf_plane_restr0.004596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.42491280.33012371X-RAY DIFFRACTION92
3.05-3.240.29811310.30752554X-RAY DIFFRACTION97
3.24-3.490.34551330.26312509X-RAY DIFFRACTION98
3.49-3.840.29471400.24032515X-RAY DIFFRACTION96
3.84-4.390.29241420.19912522X-RAY DIFFRACTION96
4.39-5.510.251450.2042477X-RAY DIFFRACTION96
5.51-19.80.27691190.22332504X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9099-0.54470.3113.8146-0.55573.3848-0.3889-0.3660.095-0.17080.05560.13580.0615-0.37880.26950.4506-0.1011-0.08620.70650.12080.5396-54.929-7.407424.5407
24.29222.198-0.11033.72290.52263.99130.2215-0.6535-0.02530.1129-0.08210.55180.07350.2342-0.08680.43060.0410.04770.46070.01350.3748-42.88688.423720.4885
30.7429-0.25980.99531.8006-0.91633.1684-0.06790.05220.2105-0.107-0.0827-0.2535-0.20220.22010.13640.3375-0.00770.01170.4107-0.04850.4505-20.488930.37812.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 207 through 253) or chain 'B'
2X-RAY DIFFRACTION2(chain 'A' and resid 254 through 299)
3X-RAY DIFFRACTION3(chain 'A' and (resid 300 through 566)) or chain 'C'

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