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

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Basic information

Entry
Database: PDB / ID: 4tnd
TitleCrystal Structure of G Protein-Coupled Receptor Kinase 5 in Complex with AMP-PNP
ComponentsG protein-coupled receptor kinase 5
KeywordsSIGNALING PROTEIN / GRK5-(5-Adenylylimidodiphosphate) complex / GRK5-(AMP-PNP) complex / GPCR Kinase / Kinase / GPCR Kinase 5
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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / G protein-coupled receptor kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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 4, 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)68,4733
Polymers67,9431
Non-polymers5312
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-12 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.975, 62.975, 292.644
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.15 M Sodium Chloride, 0.1 M BIS-TRIS pH 6.5 Crystal growth and size improved by using micro-seeding technique

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 10, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.802→47.728 Å / Num. obs: 52646 / % possible obs: 99.8 % / Redundancy: 30.4 % / Rsym value: 0.079 / Net I/σ(I): 63.85
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.8292 / Mean I/σ(I) obs: 1.17 / Rsym value: 0.851 / % possible all: 59.7

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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: 2ACX

2acx


Resolution: 1.802→47.728 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2459 4.67 %Random selection
Rwork0.1726 ---
obs0.1741 52638 94.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→47.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 32 510 4832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084417
X-RAY DIFFRACTIONf_angle_d1.1895948
X-RAY DIFFRACTIONf_dihedral_angle_d14.1961709
X-RAY DIFFRACTIONf_chiral_restr0.053621
X-RAY DIFFRACTIONf_plane_restr0.007773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8022-1.83680.2918850.26551746X-RAY DIFFRACTION61
1.8368-1.87430.2863980.22781995X-RAY DIFFRACTION69
1.8743-1.91510.26951120.22142279X-RAY DIFFRACTION79
1.9151-1.95960.24941260.2162564X-RAY DIFFRACTION88
1.9596-2.00860.25021380.19792818X-RAY DIFFRACTION97
2.0086-2.06290.20841410.18432883X-RAY DIFFRACTION100
2.0629-2.12360.19421450.18122958X-RAY DIFFRACTION100
2.1236-2.19220.23151410.17292891X-RAY DIFFRACTION100
2.1922-2.27050.22461440.17952940X-RAY DIFFRACTION100
2.2705-2.36140.23451440.1872921X-RAY DIFFRACTION100
2.3614-2.46890.2461440.18912946X-RAY DIFFRACTION100
2.4689-2.59910.24981440.18382929X-RAY DIFFRACTION100
2.5991-2.76190.19861460.1852988X-RAY DIFFRACTION100
2.7619-2.97510.22251460.18652965X-RAY DIFFRACTION100
2.9751-3.27440.23471450.18212990X-RAY DIFFRACTION100
3.2744-3.74810.18231490.16063020X-RAY DIFFRACTION100
3.7481-4.72150.15671500.13723069X-RAY DIFFRACTION100
4.7215-47.74520.17871610.163277X-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)
14.13150.61530.76563.2215-0.58294.70220.1455-0.2117-0.00260.5206-0.1942-0.2575-0.11510.3392-0.04030.2785-0.05490.04050.14970.01440.255230.9558-11.195413.0841
24.7877-0.1563-2.15590.31190.1472.07270.27030.24040.3489-0.0137-0.07550.1284-0.184-0.3717-0.14930.19270.0270.0370.1530.03040.26163.0005-10.431914.6022
31.46240.3604-0.73740.8918-0.06081.2825-0.0889-0.0535-0.22740.13810.00050.02510.35380.02420.05620.2509-0.00740.00680.11570.01640.170221.2427-37.590423.6041
41.34340.7905-0.1834.111-0.38271.0023-0.12-0.0546-0.12320.17470.11210.45490.2517-0.1296-0.00340.2855-0.04110.09110.22010.0380.25234.6248-41.067432.586
51.2665-0.0799-0.49720.60480.3441.80750.044-0.04140.18710.06680.0626-0.1056-0.16620.0955-0.0270.1202-0.0320.00240.1277-0.0070.152431.3022-20.663812.2589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 467 )
5X-RAY DIFFRACTION5chain 'A' and (resid 468 through 543 )

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