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- PDB-4g5s: Structure of LGN GL3/Galphai3 complex -

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Basic information

Entry
Database: PDB / ID: 4g5s
TitleStructure of LGN GL3/Galphai3 complex
Components
  • G-protein-signaling modulator 2
  • Guanine nucleotide-binding protein G(k) subunit alpha
KeywordsCELL CYCLE/SIGNALING PROTEIN / Galpha / GoLoco / Galpha signaling / asymmetric cell division / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / negative regulation of adenylate cyclase activity / GTP metabolic process / GDP-dissociation inhibitor activity / G protein-coupled dopamine receptor signaling pathway / dynein complex binding ...lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / G alpha (i) signalling events / negative regulation of adenylate cyclase activity / GTP metabolic process / GDP-dissociation inhibitor activity / G protein-coupled dopamine receptor signaling pathway / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of macroautophagy / lateral plasma membrane / G-protein alpha-subunit binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / mitotic spindle organization / 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 / 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 / protein domain specific binding / cell division / lysosomal membrane / nucleotide binding / GTPase activity / centrosome / nucleolus / GTP binding / Golgi apparatus / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat ...GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Tetratricopeptide repeat / Tetratricopeptide repeat / G-protein alpha subunit, group I / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily / 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
CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-3 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.62 Å
AuthorsJia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
Citation
Journal: To be Published
Title: Crystal Structures of the scaffolding protein LGN reveal the general mechanism by which GoLoco binding motifs inhibit the release of GDP from Galphai subunits in G-coupled heterotrimeric proteins
Authors: Jia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
#1: Journal: To be Published
Title: Crystal Structures of LGN-GoLoco/Galphai Complexes Reveal the General Mode of GoLoco/Galphai Interaction with a Double Arg-finger GDP Coordination
Authors: Jia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(k) subunit alpha
B: Guanine nucleotide-binding protein G(k) subunit alpha
C: Guanine nucleotide-binding protein G(k) subunit alpha
D: Guanine nucleotide-binding protein G(k) subunit alpha
E: G-protein-signaling modulator 2
G: G-protein-signaling modulator 2
Z: G-protein-signaling modulator 2
F: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,75913
Polymers163,0458
Non-polymers1,7145
Water00
1
A: Guanine nucleotide-binding protein G(k) subunit alpha
E: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3964
Polymers40,7612
Non-polymers6352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-21 kcal/mol
Surface area15460 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(k) subunit alpha
F: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2043
Polymers40,7612
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-22 kcal/mol
Surface area15360 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(k) subunit alpha
G: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3964
Polymers40,7612
Non-polymers6352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area15790 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(k) subunit alpha
Z: G-protein-signaling modulator 2


Theoretical massNumber of molelcules
Total (without water)40,7612
Polymers40,7612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-14 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.680, 209.680, 235.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Guanine nucleotide-binding protein G(k) subunit alpha / G(i) alpha-3


Mass: 37903.023 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 25-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08754
#2: Protein/peptide
G-protein-signaling modulator 2 / Pins homolog


Mass: 2858.145 Da / Num. of mol.: 4 / Fragment: GoLoco 3 (UNP RESIDUES 594-618) / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VDU0
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

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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: 4.58 Å3/Da / Density % sol: 73.16 % / Mosaicity: 0.467 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulfate, 1.0M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 35265 / Num. obs: 35082 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 120.17 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.345 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.6-3.669.40.39617200.981100
3.66-3.739.40.38817421.071100
3.73-3.89.50.33417321.0151100
3.8-3.889.60.2817190.9561100
3.88-3.969.60.24517290.9931100
3.96-4.059.60.19417441.0111100
4.05-4.169.70.1517461.0051100
4.16-4.279.70.13617351.0541100
4.27-4.399.70.12617401.0891100
4.39-4.549.60.10517641.1841100
4.54-4.79.60.08917361.341100
4.7-4.899.40.09117711.4831100
4.89-5.119.20.08817551.5261100
5.11-5.389.10.08917621.6451100
5.38-5.7190.09317741.654199.9
5.71-6.158.80.08117871.7621100
6.15-6.778.90.07417771.6861100
6.77-7.758.60.04818111.825199.7
7.75-9.758.80.03418411.653199.8
9.75-507.60.03518802.258195.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
PHENIX1.8_1063refinement
RefinementResolution: 3.62→39.626 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8065 / SU ML: 0.35 / σ(F): 1.33 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1754 5 %
Rwork0.2073 33319 -
obs0.2096 35073 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.48 Å2 / Biso mean: 129.3272 Å2 / Biso min: 33.15 Å2
Refinement stepCycle: LAST / Resolution: 3.62→39.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10116 0 110 0 10226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01710406
X-RAY DIFFRACTIONf_angle_d0.99314169
X-RAY DIFFRACTIONf_chiral_restr0.051669
X-RAY DIFFRACTIONf_plane_restr0.0061803
X-RAY DIFFRACTIONf_dihedral_angle_d13.9393557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6199-3.71770.32581200.2442492261299
3.7177-3.8270.32361140.23892519263399
3.827-3.95050.22681330.223825372670100
3.9505-4.09150.2891480.22510265899
4.0915-4.25510.22621380.18992521265999
4.2551-4.44860.24891400.1952536267699
4.4486-4.68270.22941200.17412534265499
4.6827-4.97560.24691390.17442560269999
4.9756-5.35890.22881500.188225482698100
5.3589-5.89670.27171480.219125732721100
5.8967-6.74630.32151290.250526212750100
6.7463-8.48580.25581550.219526312786100
8.4858-39.62810.22191200.20442737285797

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