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- PDB-2acx: Crystal Structure of G protein coupled receptor kinase 6 bound to... -

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Basic information

Entry
Database: PDB / ID: 2acx
TitleCrystal Structure of G protein coupled receptor kinase 6 bound to AMPPNP
ComponentsG protein-coupled receptor kinase 6
KeywordsTRANSFERASE / kINASE / g PROTEIN / grk / G PROTEIN COUPLED RECEPTOR KINASE / grk6
Function / homology
Function and homology information


G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / regulation of G protein-coupled receptor signaling pathway / regulation of signal transduction / Wnt signaling pathway / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / regulation of G protein-coupled receptor signaling pathway / regulation of signal transduction / Wnt signaling pathway / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / membrane / plasma membrane / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / PHOSPHATE ION / G protein-coupled receptor kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLodowski, D.T. / Tesmer, V.M. / Benovic, J.L. / Tesmer, J.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structure of G Protein-coupled Receptor Kinase (GRK)-6 Defines a Second Lineage of GRKs.
Authors: Lodowski, D.T. / Tesmer, V.M. / Benovic, J.L. / Tesmer, J.J.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 999SEQUENCE THE DISCREPANCIES AT RESIDUES 60 AND 104 IN SWISS-PROT P43250 ARE DUE TO ERRORS IN THE ...SEQUENCE THE DISCREPANCIES AT RESIDUES 60 AND 104 IN SWISS-PROT P43250 ARE DUE TO ERRORS IN THE SEQUENCE, ACCORDING TO THE AUTHORS.

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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 6
B: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2728
Polymers132,0212
Non-polymers1,2516
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-42 kcal/mol
Surface area47810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.164, 59.270, 221.095
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSER2AA24 - 53224 - 532
21LYSLYSPROPRO2BB24 - 53524 - 535
12HOHHOHHOHHOH1AI580 - 585
22HOHHOHHOHHOH1BJ580 - 585
13LYSLYSARGARG4AA14 - 1614 - 16
23LYSLYSARGARG4BB14 - 1614 - 16
14ANPANPMGMG4AE - C577 - 578
24ANPANPMGMG4BH - F577 - 578

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein G protein-coupled receptor kinase 6 / G protein-coupled receptor kinase GRK6


Mass: 66010.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRK6, GPRK6 / Cell line (production host): Hi-9 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P43250, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: peg 3350, MALIC ACID, sODIUM CHLORIDE, MAGNESIUM CHLORIDE, amppnp, ethylene glycol , pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2004 / Details: Double crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 44832 / Num. obs: 43666 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rsym value: 0.06 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.501 / % possible all: 90.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT1.7data extraction
Adxvdata processing
ELVESdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMW (GRK2)

1omw


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 25.503 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.457 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24261 2317 5 %RANDOM
Rwork0.20175 ---
obs0.2039 43666 97.39 %-
all-45983 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-2.34 Å2
2--3.87 Å20 Å2
3----4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7995 0 74 37 8106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228253
X-RAY DIFFRACTIONr_bond_other_d0.0030.027467
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.96611125
X-RAY DIFFRACTIONr_angle_other_deg0.921317412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94123.284402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.01151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441575
X-RAY DIFFRACTIONr_chiral_restr0.0930.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029034
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021735
X-RAY DIFFRACTIONr_nbd_refined0.2320.21797
X-RAY DIFFRACTIONr_nbd_other0.1890.27460
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23988
X-RAY DIFFRACTIONr_nbtor_other0.0930.25098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.56298
X-RAY DIFFRACTIONr_mcbond_other0.1461.51987
X-RAY DIFFRACTIONr_mcangle_it1.12127916
X-RAY DIFFRACTIONr_scbond_it1.79133899
X-RAY DIFFRACTIONr_scangle_it2.7484.53209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
112857tight positional0.050.05
226tight positional0.090.05
114739medium positional0.460.5
3155medium positional0.610.5
4143medium positional0.240.5
112857tight thermal1.910
226tight thermal3.3410
114739medium thermal2.1915
3155medium thermal1.2315
4143medium thermal2.7715
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 148 -
Rwork0.329 2895 -
obs--89.21 %
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)
12.1234-0.87730.75981.9732-0.68013.0986-0.0617-0.2135-0.0550.04220.1005-0.0294-0.0327-0.0359-0.0388-0.22590.06640.0054-0.2533-0.0547-0.2511-12.902714.417735.6469
23.2937-0.35620.40351.3564-0.11383.1217-0.0922-0.4642-0.19110.14420.1652-0.02260.10470.2208-0.073-0.07010.19510.00580.20920.0627-0.17752.35292.638571.2468
32.67710.37621.56762.6194-1.3144.0561-0.081-0.07040.3289-0.0076-0.0405-0.049-0.42080.17150.1214-0.22080.0350.0169-0.4989-0.051-0.2194-19.880328.855611.7637
42.1898-0.58811.04673.60170.5174.57650.0913-0.661-0.21270.64720.0244-0.42290.16320.4895-0.11570.14470.1773-0.0760.83930.0528-0.058315.31381.406196.6519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 26614 - 266
2X-RAY DIFFRACTION1AA492 - 527492 - 527
3X-RAY DIFFRACTION1AG - C577 - 5781
4X-RAY DIFFRACTION1BB528 - 535528 - 535
5X-RAY DIFFRACTION1AI580 - 6091 - 30
6X-RAY DIFFRACTION2BB14 - 26614 - 266
7X-RAY DIFFRACTION2BB492 - 527492 - 527
8X-RAY DIFFRACTION2BH - D577 - 5781
9X-RAY DIFFRACTION2AA528 - 532528 - 532
10X-RAY DIFFRACTION2BJ580 - 5861 - 7
11X-RAY DIFFRACTION3AA267 - 474267 - 474
12X-RAY DIFFRACTION4BB267 - 473267 - 473

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