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- PDB-2g83: Structure of activated G-alpha-i1 bound to a nucleotide-state-sel... -

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Basic information

Entry
Database: PDB / ID: 2g83
TitleStructure of activated G-alpha-i1 bound to a nucleotide-state-selective peptide: Minimal determinants for recognizing the active form of a G protein alpha subunit
Components
  • Guanine nucleotide-binding protein G(i), alpha-1 subunit
  • KB-1753 phage display peptide
KeywordsSIGNALING PROTEIN / Guanine-nucleotide binding protein / Phage display peptide
Function / homology
Function and homology information


Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding ...Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohnston, C.A. / Ramer, J.K. / Blaesius, R. / Kuhlman, B. / Arshavsky, V.Y. / Siderovski, D.P.
CitationJournal: Biochemistry / Year: 2006
Title: Minimal Determinants for Binding Activated Galpha from the Structure of a Galpha(i1)-Peptide Dimer.
Authors: Johnston, C.A. / Lobanova, E.S. / Shavkunov, A.S. / Low, J. / Ramer, J.K. / Blaesius, R. / Fredericks, Z. / Willard, F.S. / Kuhlman, B. / Arshavsky, V.Y. / Siderovski, D.P.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_conn_type.id / _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: Guanine nucleotide-binding protein G(i), alpha-1 subunit
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: KB-1753 phage display peptide
D: KB-1753 phage display peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,55410
Polymers74,4134
Non-polymers1,1416
Water54030
1
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
C: KB-1753 phage display peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7775
Polymers37,2062
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanine nucleotide-binding protein G(i), alpha-1 subunit
D: KB-1753 phage display peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7775
Polymers37,2062
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-24 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.130, 103.130, 206.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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

#1: Protein Guanine nucleotide-binding protein G(i), alpha-1 subunit / Adenylate cyclase-inhibiting G alpha protein


Mass: 35867.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Plasmid: pPRO-ExHtb1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63096
#2: Protein/peptide KB-1753 phage display peptide


Mass: 1338.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Phage-derived peptide

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Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG-8000, 0.3M calcium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 32367 / Num. obs: 30456 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 61

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GFI

1gfi


Resolution: 2.8→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3 2824 Random
Rwork0.269 --
all0.27 32139 -
obs0.301 28276 -
Displacement parametersBiso mean: 58.958 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 68 30 5190

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