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- PDB-3uzs: Structure of the C13.28 RNA Aptamer Bound to the G Protein-Couple... -

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Basic information

Entry
Database: PDB / ID: 3uzs
TitleStructure of the C13.28 RNA Aptamer Bound to the G Protein-Coupled Receptor Kinase 2-Heterotrimeric G Protein Beta 1 and Gamma 2 Subunit Complex
Components
  • Beta-adrenergic receptor kinase 1
  • C13.28 RNA Aptamer
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsTRANSFERASE/RNA / Protein-RNA complex / Protein Kinase Fold / RGS Homology Domain / Pleckstrin Homology Domain / beta propeller / G Protein-Coupled Receptor Phosphorylation / RNA Aptamer / Carboxymethylation / geranylgeranylation / TRANSFERASE-RNA complex
Function / homology
Function and homology information


Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway ...Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / negative regulation of striated muscle contraction / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Cargo recognition for clathrin-mediated endocytosis / positive regulation of protein localization to cilium / desensitization of G protein-coupled receptor signaling pathway / cytoplasmic side of mitochondrial outer membrane / Activation of the phototransduction cascade / regulation of the force of heart contraction / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of signal transduction / cardiac muscle contraction / adenylate cyclase-activating adrenergic receptor signaling pathway / viral genome replication / cell projection / intracellular protein transport / G protein-coupled receptor binding / G protein-coupled acetylcholine receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / presynapse / signaling receptor complex adaptor activity / heart development / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / protein phosphorylation / protein kinase activity / postsynapse / G protein-coupled receptor signaling pathway / GTPase activity / synapse / symbiont entry into host cell / protein-containing complex binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / PH-like domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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
RNA / RNA (> 10) / Beta-adrenergic receptor kinase 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.52 Å
AuthorsTesmer, J.J.G. / Tesmer, V.M.
CitationJournal: Structure / Year: 2012
Title: Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer.
Authors: Tesmer, V.M. / Lennarz, S. / Mayer, G. / Tesmer, J.J.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / 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_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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: Beta-adrenergic receptor kinase 1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
C: C13.28 RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,6775
Polymers134,6534
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-63 kcal/mol
Surface area56320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.277, 257.277, 99.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312

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Components

#1: Protein Beta-adrenergic receptor kinase 1 / Beta-ARK-1 / G-protein-coupled receptor kinase 2


Mass: 79749.922 Da / Num. of mol.: 1 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ADRBK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21146, beta-adrenergic-receptor kinase
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 8406.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63212
#4: RNA chain C13.28 RNA Aptamer


Mass: 9079.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA polymer, no 5' or 3' phosphates
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 7.05 Å3/Da / Density % sol: 82.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM NaCl and 3% PEG 8000, 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: RAYONIX MX-300 / Detector: CCD / Date: Jul 1, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 12758 / % possible obs: 58.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.064 / Net I/σ(I): 24.5
Reflection shellResolution: 4.5→4.58 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.388 / % possible all: 9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMW

1omw


Resolution: 4.52→19.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.919 / SU B: 178.994 / SU ML: 0.951 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 1.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26837 650 5.2 %RANDOM
Rwork0.18351 ---
obs0.18758 11919 56.92 %-
all-11919 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 282.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 4.52→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 423 1 0 8535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198773
X-RAY DIFFRACTIONr_bond_other_d0.0010.025982
X-RAY DIFFRACTIONr_angle_refined_deg0.8561.92711892
X-RAY DIFFRACTIONr_angle_other_deg0.764314515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83851009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58623.835399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27151497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2491563
X-RAY DIFFRACTIONr_chiral_restr0.0490.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021835
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.517→4.628 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 6 -
Rwork0.268 154 -
obs--10.74 %
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)
13.8568-0.4711-0.24163.23591.58411.2226-0.13360.33850.17570.0461-0.05180.4132-1.0848-0.46410.18543.04810.97610.64740.60180.05671.629992.08314.82834.663
23.99572.9094-5.95245.2659-5.532813.08430.73510.0126-0.2820.3542-0.3856-0.1878-1.70480.1339-0.34951.01180.12270.43230.27520.02150.9764113.958-13.06522.119
36.36342.7056-0.63128.5818-0.724410.27820.9944-0.03790.07350.70080.10471.0422-0.0197-0.6398-1.09920.67880.41120.5110.53350.45391.051990.512-38.4838.824
44.51283.06330.94055.5243-0.03277.0439-0.26920.0314-0.2769-2.07250.2904-0.07570.7537-0.2989-0.02121.3930.06140.07910.2968-0.05920.906391.761-71.14124.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A185 - 513
2X-RAY DIFFRACTION1A701
3X-RAY DIFFRACTION1C41 - 68
4X-RAY DIFFRACTION2A29 - 184
5X-RAY DIFFRACTION2A514 - 545
6X-RAY DIFFRACTION3A546 - 671
7X-RAY DIFFRACTION4B2 - 340
8X-RAY DIFFRACTION4G2 - 68

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