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- PDB-3nyn: Crystal Structure of G Protein-Coupled Receptor Kinase 6 in Compl... -

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Basic information

Entry
Database: PDB / ID: 3nyn
TitleCrystal Structure of G Protein-Coupled Receptor Kinase 6 in Complex with Sangivamycin
ComponentsG protein-coupled receptor kinase 6
KeywordsTRANSFERASE / Kinase / GRK / RGS homology domain / G protein-coupled receptor kinase
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2260 / Helix Hairpins - #1270 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2260 / Helix Hairpins - #1270 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Helix non-globular / Special / Helix Hairpins / 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
(R,R)-2,3-BUTANEDIOL / SANGIVAMYCIN / G protein-coupled receptor kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsTesmer, J.J.G. / Singh, P.
CitationJournal: Embo J. / Year: 2010
Title: Molecular basis for activation of G protein-coupled receptor kinases.
Authors: Boguth, C.A. / Singh, P. / Huang, C.C. / Tesmer, J.J.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_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

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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)134,10720
Polymers131,9642
Non-polymers2,14418
Water21612
1
A: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05410
Polymers65,9821
Non-polymers1,0729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G protein-coupled receptor kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05410
Polymers65,9821
Non-polymers1,0729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-194 kcal/mol
Surface area54530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.590, 154.590, 207.914
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SO4 / End label comp-ID: SO4 / Refine code: 2 / Auth seq-ID: 3 - 585 / Label seq-ID: 3

Dom-IDAuth asym-IDLabel asym-ID
1AA - K
2BB - T

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Components

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


Mass: 65981.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPRK6, GRK6 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five
References: UniProt: P43250, 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.: 2 / Source method: obtained synthetically / Formula: C12H15N5O5 / Comment: inhibitor*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 5.62 Å3/Da / Density % sol: 78.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10 mg/ml GRK6 mixed 1:1 with well containing 1.9 M AMS and 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 77021 / Num. obs: 45850 / % possible obs: 59.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.7-2.754.80.3511.2
2.75-2.84.30.3684
2.8-2.854.10.3237
2.85-2.913.90.31310.5
2.91-2.973.90.35114.7
2.97-3.0440.32419.3
3.04-3.1240.34325
3.12-3.23.90.28432.5
3.2-3.33.90.28940.6
3.3-3.43.90.26654
3.4-3.523.90.2678.7
3.52-3.663.80.228100
3.66-3.833.80.198100
3.83-4.033.80.156100
4.03-4.283.80.107100
4.28-4.623.80.078100
4.62-5.083.80.075100
5.08-5.813.80.082100
5.81-7.313.80.0699.9
7.31-403.70.04198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→30 Å / Cor.coef. Fo:Fc: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.953 / SU ML: 0.201 / SU R Cruickshank DPI: 0.7014 / ESU R: 0.709 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 2284 -RANDOM
Rwork0.22709 ---
obs0.22709 45750 60.43 %-
all-43466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.517 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å22.38 Å20 Å2
2--4.75 Å20 Å2
3----7.13 Å2
Refinement stepCycle: LAST / Resolution: 2.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8908 0 126 12 9046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229224
X-RAY DIFFRACTIONr_bond_other_d0.0010.026586
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9912452
X-RAY DIFFRACTIONr_angle_other_deg0.754315956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1351102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21923.591440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.162151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4311578
X-RAY DIFFRACTIONr_chiral_restr0.0540.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02110088
X-RAY DIFFRACTIONr_gen_planes_other00.021890
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.55518
X-RAY DIFFRACTIONr_mcbond_other0.0681.52226
X-RAY DIFFRACTIONr_mcangle_it1.63928888
X-RAY DIFFRACTIONr_scbond_it0.76533706
X-RAY DIFFRACTIONr_scangle_it1.3654.53564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3239tight positional0.180.05
4553medium positional0.330.5
3239tight thermal0.190.5
4553medium thermal0.222
LS refinement shellResolution: 2.715→2.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.495 154 -
Rfree-0 -
obs--2.78 %
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)
10.06180.00810.07560.0320.15531.286-0.05980.05410.0677-0.0196-0.0221-0.01050.3276-0.01960.08180.45540.00090.0260.13790.03950.1223-72.709825.699620.488
20.61280.01420.47341.65690.30122.3128-0.09670.07770.12110.06250.081-0.0388-0.40640.74730.01570.2212-0.2375-0.06610.4045-0.0170.0851-51.264750.342613.587
30.86110.3829-0.55920.2247-0.32131.2737-0.28490.28080.0214-0.03550.1110.0482-0.10160.22660.17390.3198-0.2546-0.00850.49020.10170.1176-56.177750.6771-42.5833
40.0485-0.05060.0353.14671.35960.65860.06730.1041-0.0612-0.1544-0.07420.2394-0.00590.11340.0070.54880.01160.01480.294-0.18040.1258-65.710519.5926-34.8066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 74
2X-RAY DIFFRACTION1A155 - 527
3X-RAY DIFFRACTION1A576 - 585
4X-RAY DIFFRACTION1B528 - 543
5X-RAY DIFFRACTION1C1 - 7
6X-RAY DIFFRACTION2A75 - 154
7X-RAY DIFFRACTION2B544 - 557
8X-RAY DIFFRACTION3B1 - 74
9X-RAY DIFFRACTION3B155 - 527
10X-RAY DIFFRACTION3B576 - 585
11X-RAY DIFFRACTION3A528 - 543
12X-RAY DIFFRACTION3D1 - 6
13X-RAY DIFFRACTION4B75 - 154
14X-RAY DIFFRACTION4A544 - 557

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