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- PDB-9cko: Human G protein-coupled receptor kinase 5 wild-type in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9cko
TitleHuman G protein-coupled receptor kinase 5 wild-type in complex with sangivamycin
ComponentsG protein-coupled receptor kinase 5
KeywordsSIGNALING PROTEIN / GPCR / GRK / G protein-coupled receptor / G protein-coupled receptor kinase / GPCR signaling
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 / regulation of signal transduction / fat cell differentiation / 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 / regulation of signal transduction / fat cell differentiation / 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 / apoptotic process / positive regulation of cell population proliferation / 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
ACETYL GROUP / : / SANGIVAMYCIN / 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, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
CitationJournal: To Be Published
Title: Structures of G protein-coupled receptor kinase 5 in multiple conformations reveals mechanism of activation and inhibition
Authors: Chen, Y. / Tesmer, J.J.G.
History
DepositionJul 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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)69,3254
Polymers68,9331
Non-polymers3923
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.259, 140.259, 78.766
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 / G protein-coupled receptor kinase GRK5


Mass: 68932.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5, GPRK5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P34947, G-protein-coupled receptor kinase
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SGV / SANGIVAMYCIN / 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide


Mass: 309.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200mM potassium citrate tribasic, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.67→62.73 Å / Num. obs: 22966 / % possible obs: 99.96 % / Redundancy: 13.4 % / Biso Wilson estimate: 71.91 Å2 / Rmerge(I) obs: 0.247 / Net I/σ(I): 7.7
Reflection shellResolution: 2.73→2.8 Å / Num. unique obs: 2242 / CC1/2: 0.85

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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→29.45 Å / SU ML: 0.5063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2804 1734 8.73 %
Rwork0.2396 18138 -
obs0.2432 19872 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 26 72 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434506
X-RAY DIFFRACTIONf_angle_d0.57316065
X-RAY DIFFRACTIONf_chiral_restr0.0398640
X-RAY DIFFRACTIONf_plane_restr0.0064790
X-RAY DIFFRACTIONf_dihedral_angle_d23.00961761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.47891430.45881486X-RAY DIFFRACTION100
2.88-2.980.391410.38071484X-RAY DIFFRACTION100
2.98-3.080.38951410.34941469X-RAY DIFFRACTION99.94
3.08-3.20.32951430.30931497X-RAY DIFFRACTION99.94
3.21-3.350.35131410.30661490X-RAY DIFFRACTION100
3.35-3.530.35981420.30271483X-RAY DIFFRACTION99.88
3.53-3.750.31431440.24531507X-RAY DIFFRACTION99.94
3.75-4.040.30911440.22081495X-RAY DIFFRACTION100
4.04-4.440.25121440.19871512X-RAY DIFFRACTION99.94
4.44-5.080.21431460.18741527X-RAY DIFFRACTION100
5.08-6.390.24881480.21211551X-RAY DIFFRACTION100
6.39-29.450.2231570.2011637X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: -33.8331297714 Å / Origin y: 5.30366258802 Å / Origin z: 14.5317187411 Å
111213212223313233
T0.409576988867 Å20.00517631742178 Å2-0.026474196838 Å2-0.510536624553 Å2-0.146403391472 Å2--0.306337485184 Å2
L0.778512812114 °2-0.569944083773 °2-0.227569149584 °2-2.92528558528 °2-0.0632788357761 °2--0.708174707864 °2
S-0.00976124132432 Å °-0.0124542210371 Å °0.0216145771383 Å °0.00419811801849 Å °0.129313252221 Å °-0.396618792894 Å °0.0900502723762 Å °0.113590157852 Å °-0.0789068878511 Å °
Refinement TLS groupSelection details: all

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