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- PDB-9bro: Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 in... -

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Basic information

Entry
Database: PDB / ID: 9bro
TitleCrystal Structure of Human G Protein-Coupled Receptor Kinase 5 in Complex with GRL030-22
ComponentsG protein-coupled receptor kinase 5
KeywordsSIGNALING PROTEIN/INHIBITOR / G protein-coupled receptor / GPCR G protein-coupled receptor kinase / GRK kinase / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / phospholipid binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / phospholipid binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Wnt signaling pathway / protein autophosphorylation / nuclear membrane / G alpha (s) signalling events / G alpha (q) signalling events / protein kinase activity / regulation of cell cycle / nuclear speck / G protein-coupled receptor signaling pathway / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GPCR kinase / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...GPCR kinase / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / G protein-coupled receptor kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, Y. / Tesmer, J.J.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)CA023168 United States
CitationJournal: To Be Published
Title: Structure of GRK5 in complex with novel inhibitors
Authors: Chen, Y. / Tesmer, J.J.G.
History
DepositionMay 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G protein-coupled receptor kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4322
Polymers68,9321
Non-polymers5011
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-3 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.397, 139.397, 71.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein G protein-coupled receptor kinase 5


Mass: 68931.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P34947
#2: Chemical ChemComp-A1ARE / (3Z)-3-[(4-{[(2S)-1-methoxypropan-2-yl]carbamoyl}-3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-2-oxo-N-[(1R)-1-phenylethyl]-3,7-dihydro-2H-indole-5-carboxamide


Mass: 500.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 220 mM potassium citrate tribasic, 20% PEG3350, crystals soaked in 25% PEG3350, 10% glycerol, 1 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.58→63.68 Å / Num. obs: 22713 / % possible obs: 99.96 % / Redundancy: 12.1 % / Biso Wilson estimate: 83.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 2.58→2.62 Å / Num. unique obs: 1120 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.87 Å / SU ML: 0.5116 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.5552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2713 1582 8.83 %
Rwork0.2165 16339 -
obs0.2212 17921 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 37 43 4172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274222
X-RAY DIFFRACTIONf_angle_d0.50385683
X-RAY DIFFRACTIONf_chiral_restr0.0377589
X-RAY DIFFRACTIONf_plane_restr0.004741
X-RAY DIFFRACTIONf_dihedral_angle_d18.63731621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.56841390.4511448X-RAY DIFFRACTION100
2.89-2.990.45881430.34071462X-RAY DIFFRACTION100
2.99-3.110.37321400.30031451X-RAY DIFFRACTION100
3.11-3.250.32381410.28381464X-RAY DIFFRACTION100
3.25-3.430.32791430.28981465X-RAY DIFFRACTION100
3.43-3.640.31371410.27621464X-RAY DIFFRACTION100
3.64-3.920.3241430.24361473X-RAY DIFFRACTION99.81
3.92-4.310.22181430.18491476X-RAY DIFFRACTION100
4.31-4.940.1991460.15981503X-RAY DIFFRACTION100
4.94-6.210.21841470.19651520X-RAY DIFFRACTION100
6.21-29.870.24921560.17551613X-RAY DIFFRACTION100
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)
14.672520831550.814715757752-0.447298763364.05873206162-0.4385073952664.56831528344-0.1186770800270.029635560434-0.07871210831540.1700637000650.004513982828570.308491850434-0.157625891974-0.2610718213390.1129793478090.635512080385-0.0133724770938-0.04728678857360.4699798274020.1130794350730.49743607579435.242378741217.901328091311.206721349
22.297883746831.69147553316-0.01303453775924.14777431856-0.1827222482382.01538382727-0.07359847307960.2102837617360.0183237097873-0.3963460763920.1325825386920.121631226630.0446772137547-0.120377559643-0.04567803873330.5181242224340.07815253943-0.001996163542850.3472695624080.0345219740760.3421499269530.0030366678-2.86039828773.03036022894
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 240 )25 - 2401 - 216
22chain 'A' and (resid 241 through 542 )241 - 542217 - 503

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