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- PDB-9ckp: Human G protein-coupled receptor kinase 5-D311N in complex with s... -

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Basic information

Entry
Database: PDB / ID: 9ckp
TitleHuman G protein-coupled receptor kinase 5-D311N 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 / 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 / cytosol / cytoplasm
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: 2.6 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)69,3244
Polymers68,9321
Non-polymers3923
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.206, 140.206, 77.832
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 / Mutation: D311N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P34947
#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
#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.: 47 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 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: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.33→62.7 Å / Num. obs: 33722 / % possible obs: 99.81 % / Redundancy: 13.5 % / Biso Wilson estimate: 62.13 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 9.6
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 3262 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.25 Å / SU ML: 0.3969 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.2265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 1452 5.96 %
Rwork0.2342 22918 -
obs0.2363 24370 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 26 47 4445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614490
X-RAY DIFFRACTIONf_angle_d0.57776042
X-RAY DIFFRACTIONf_chiral_restr0.0405638
X-RAY DIFFRACTIONf_plane_restr0.0061786
X-RAY DIFFRACTIONf_dihedral_angle_d20.8591756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.40041430.34582248X-RAY DIFFRACTION100
2.69-2.80.31461420.32072248X-RAY DIFFRACTION99.96
2.8-2.930.37461420.32592251X-RAY DIFFRACTION99.96
2.93-3.080.31641430.31212257X-RAY DIFFRACTION99.79
3.08-3.270.33871440.28652258X-RAY DIFFRACTION99.83
3.28-3.530.34571440.26772271X-RAY DIFFRACTION100
3.53-3.880.28271450.23772301X-RAY DIFFRACTION100
3.88-4.440.23261470.19772296X-RAY DIFFRACTION99.96
4.44-5.590.21351480.19682338X-RAY DIFFRACTION100
5.59-29.250.22891540.19922450X-RAY DIFFRACTION99.69
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)
10.8086237231770.1779075180270.08904623876832.97402987814-0.1447644472240.597469024391-0.07069891506840.312837444577-0.108687003702-0.5769849929140.112586277953-0.4252266559950.03854570111710.06667153252080.003336074807060.46637802348-0.01688190399220.150582994610.590526121841-0.1208558515950.523601061202-35.391308939621.51467792474.15060088892
21.25355943571-1.11274711859-0.6915111950073.251916294370.5762305360440.688965002994-0.162892348621-0.3232976489120.2775716508050.2403678613150.426016796253-0.7264139716370.1228575555930.32009130688-0.2068705457110.408935261520.0280935092707-0.1076282473360.548205970985-0.250488313850.632454407792-32.796159761-3.0310599540619.6913124927
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 177 )1 - 1772 - 174
22chain 'A' and (resid 178 through 542 )178 - 542175 - 539

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