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- PDB-1kjy: Crystal Structure of Human G[alpha]i1 Bound to the GoLoco Motif o... -

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Basic information

Entry
Database: PDB / ID: 1kjy
TitleCrystal Structure of Human G[alpha]i1 Bound to the GoLoco Motif of RGS14
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
  • REGULATOR OF G-PROTEIN SIGNALING 14
KeywordsSIGNALING PROTEIN / Protein-peptide complex
Function / homology
Function and homology information


zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / G alpha (i) signalling events / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / G alpha (i) signalling events / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / G-protein alpha-subunit binding / T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / long-term memory / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / negative regulation of MAP kinase activity / regulation of mitotic spindle organization / cellular response to forskolin / GTPase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / learning / chromosome segregation / Regulation of insulin secretion / G protein-coupled receptor binding / long-term synaptic potentiation / modulation of chemical synaptic transmission / visual learning / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / PML body / negative regulation of ERK1 and ERK2 cascade / response to peptide hormone / spindle pole / ADP signalling through P2Y purinoceptor 12 / spindle / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / mitotic cell cycle / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule binding / response to oxidative stress / microtubule / Extra-nuclear estrogen signaling / dendritic spine / postsynaptic density / nuclear body / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / glutamatergic synapse / dendrite / nucleolus / GTP binding / protein kinase binding / magnesium ion binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like ...RGS14, RGS domain / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / RGS, subdomain 1/3 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Ubiquitin-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 14 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKimple, R.J. / Kimple, M.E. / Betts, L. / Sondek, J. / Siderovski, D.P.
CitationJournal: Nature / Year: 2002
Title: Structural determinants for GoLoco-induced inhibition of nucleotide release by Galpha subunits.
Authors: Kimple, R.J. / Kimple, M.E. / Betts, L. / Sondek, J. / Siderovski, D.P.
History
DepositionDec 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS CORRECT AND THAT RESIDUE 30 IS GLY FOR CHAINS A & B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
B: REGULATOR OF G-PROTEIN SIGNALING 14
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
D: REGULATOR OF G-PROTEIN SIGNALING 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,43523
Polymers82,5064
Non-polymers2,92919
Water3,711206
1
A: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
B: REGULATOR OF G-PROTEIN SIGNALING 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65111
Polymers41,2532
Non-polymers1,3989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-197 kcal/mol
Surface area16210 Å2
MethodPISA
2
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
D: REGULATOR OF G-PROTEIN SIGNALING 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,78412
Polymers41,2532
Non-polymers1,53110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-220 kcal/mol
Surface area16340 Å2
MethodPISA
3
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
D: REGULATOR OF G-PROTEIN SIGNALING 14
hetero molecules

A: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT
B: REGULATOR OF G-PROTEIN SIGNALING 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,43523
Polymers82,5064
Non-polymers2,92919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+1,y+1,-z+1/21
Buried area13070 Å2
ΔGint-427 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.510, 82.040, 187.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-4185-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT / ADENYLATE CYCLASE-INHIBITING G ALPHA PROTEIN


Mass: 37159.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPROexHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63096
#2: Protein/peptide REGULATOR OF G-PROTEIN SIGNALING 14 / RGS14


Mass: 4093.621 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Rattus norvegicus (rat).
References: UniProt: O08773

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Non-polymers , 4 types, 225 molecules

#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Cesium Sulfate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1dropand 1.5-fold molar excess R14GL peptide
210 mMTris1droppH7.5
31 mM1dropMgCl2
40.010 mMGDP1drop
55 %glycerol1drop
6100 mMsodium acetate1reservoirpH4.6
710 %glycerol1reservoir
81.4 Mcaesium sulphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 17, 2001 / Details: Osmic Confocal Blue
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 136468 / % possible obs: 99.1 % / Observed criterion σ(I): 2.5 / Redundancy: 4.6 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.088 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2875 / Rsym value: 0.45 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 29900 / Num. measured all: 136468 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 97.5 % / Num. unique obs: 2875 / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BOF

1bof


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1706201.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1477 4.9 %RANDOM
Rwork0.238 ---
all-29842 --
obs-29842 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.227 Å2 / ksol: 0.340631 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å20 Å20 Å2
2--1 Å20 Å2
3---3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 73 206 5916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 242 5 %
Rwork0.313 4574 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMGDP.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4GDP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.238 / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.383 / Rfactor Rwork: 0.313 / Rfactor obs: 0.313

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