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- PDB-4tnb: Crystal Structure of G Protein-Coupled Receptor Kinase 5 in Compl... -

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Basic information

Entry
Database: PDB / ID: 4tnb
TitleCrystal Structure of G Protein-Coupled Receptor Kinase 5 in Complex with Sangivamycin
ComponentsG protein-coupled receptor kinase 5
KeywordsSIGNALING PROTEIN / GRK5-Sangivamycin complex / GPCR Kinase / Kinase / inhibitor
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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipid binding ...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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipid binding / Wnt signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / nuclear membrane / protein autophosphorylation / regulation of cell cycle / protein kinase activity / 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 / cytosol / cytoplasm
Similarity search - Function
GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases ...GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SANGIVAMYCIN / G protein-coupled receptor kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsBhardwaj, A. / Komolov, K.E. / Benovic, J.L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Atomic Structure of G Protein-Coupled Receptor Kinase 5 (GRK5) Reveals Distinct Structural Features Novel for GRKs.
Authors: Komolov, K.E. / Bhardwaj, A. / Benovic, J.L.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,2522
Polymers67,9431
Non-polymers3091
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.676, 62.676, 292.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein G protein-coupled receptor kinase 5 / G protein-coupled receptor kinase GRK5


Mass: 67942.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5, GPRK5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P34947, G-protein-coupled receptor kinase
#2: Chemical ChemComp-SGV / SANGIVAMYCIN / 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide / Sangivamycin


Mass: 309.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O5 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% PEG 3350, 0.15 M Sodium Chloride, 0.1 M BIS-TRIS pH 5.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2013 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.113→47.567 Å / Num. obs: 28334 / % possible obs: 83.7 % / Redundancy: 3.6 % / Rsym value: 0.112 / Net I/σ(I): 12.64
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.34 / Rsym value: 0.426 / % possible all: 51.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NYN

3nyn


Resolution: 2.113→47.567 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1999 7.06 %
Rwork0.1703 --
obs0.1747 28334 81.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.113→47.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 22 398 4710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084408
X-RAY DIFFRACTIONf_angle_d1.1795932
X-RAY DIFFRACTIONf_dihedral_angle_d14.5431703
X-RAY DIFFRACTIONf_chiral_restr0.049619
X-RAY DIFFRACTIONf_plane_restr0.006774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.113-2.16550.3494540.2296703X-RAY DIFFRACTION31
2.1655-2.22410.284920.22291215X-RAY DIFFRACTION54
2.2241-2.28950.28391220.22541623X-RAY DIFFRACTION73
2.2895-2.36340.24251510.21711988X-RAY DIFFRACTION88
2.3634-2.44790.31941580.20952085X-RAY DIFFRACTION92
2.4479-2.54590.26741590.20462084X-RAY DIFFRACTION92
2.5459-2.66170.29551570.19912061X-RAY DIFFRACTION91
2.6617-2.8020.27071570.19162083X-RAY DIFFRACTION91
2.802-2.97760.25231590.19512094X-RAY DIFFRACTION91
2.9776-3.20740.25561560.19142041X-RAY DIFFRACTION90
3.2074-3.53010.23791560.17192076X-RAY DIFFRACTION89
3.5301-4.04070.21041580.14762068X-RAY DIFFRACTION88
4.0407-5.08990.18511560.12252054X-RAY DIFFRACTION87
5.0899-47.57940.17511640.1412160X-RAY DIFFRACTION84
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)
11.17560.3454-0.06361.0077-0.3430.47880.1502-0.00150.14260.0788-0.1633-0.0426-0.12520.0302-0.00150.3108-0.02020.02650.2202-0.00650.283122.6214-10.742811.499
21.37730.0156-0.66470.1152-0.12440.45820.14090.19480.0653-0.0086-0.04590.0976-0.1306-0.2261-0.00020.29480.00220.03390.2676-0.00240.31430.8158-10.351815.7964
31.16520.2014-0.78740.6396-0.06871.30380.0225-0.0377-0.07380.1231-0.0222-0.01830.19140.074100.2805-0.02-0.00720.21370.00820.236223.776-33.705622.5134
41.0030.5721-0.56921.9628-0.62951.0725-0.14020.019-0.1279-0.09430.07430.12910.1511-0.0896-0.010.3389-0.07760.04560.23620.00190.317.6755-44.381430.5659
50.8382-0.3321-0.33850.377-0.09920.7193-0.0269-0.08310.02470.03170.10130.0167-0.13980.03370.13250.1657-0.02570.00890.1464-0.01180.136531.1864-20.507512.1976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 343 through 467 )
5X-RAY DIFFRACTION5chain 'A' and (resid 468 through 543 )

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