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- PDB-4g5r: Structure of LGN GL4/Galphai3 complex -

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Basic information

Entry
Database: PDB / ID: 4g5r
TitleStructure of LGN GL4/Galphai3 complex
Components
  • G-protein-signaling modulator 2
  • Guanine nucleotide-binding protein G(k) subunit alpha
KeywordsCELL CYCLE/SIGNALING PROTEIN / Galphai / GoLoco / Galpha signaling / asymmetric cell division / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Ran protein signal transduction / 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 / dopamine receptor signaling pathway ...Ran protein signal transduction / 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 / dopamine receptor signaling pathway / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / 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 / cell division / lysosomal membrane / protein domain specific binding / nucleotide binding / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
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: 3.481 Å
AuthorsJia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
CitationJournal: 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.
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
F: G-protein-signaling modulator 2
G: G-protein-signaling modulator 2
Z: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,84019
Polymers164,0108
Non-polymers2,82911
Water0
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)41,5424
Polymers41,0032
Non-polymers5392
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-29 kcal/mol
Surface area15710 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)41,9266
Polymers41,0032
Non-polymers9244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-34 kcal/mol
Surface area15690 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)41,9266
Polymers41,0032
Non-polymers9244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-30 kcal/mol
Surface area16170 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(k) subunit alpha
Z: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4463
Polymers41,0032
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-19 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.550, 209.550, 237.211
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 / LGN / Pins homolog


Mass: 3099.544 Da / Num. of mol.: 4 / Fragment: GoLoco 4 (UNP RESIDUES 628-653) / 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 / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / 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 %
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: Nov 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.48→50 Å / Num. all: 39388 / Num. obs: 39267 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 95.39 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1955

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.8_1063refinement
RefinementResolution: 3.481→48.044 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8099 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 25.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1962 5.01 %
Rwork0.2091 37183 -
obs0.2113 39145 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.31 Å2 / Biso mean: 103.2263 Å2 / Biso min: 37.1 Å2
Refinement stepCycle: LAST / Resolution: 3.481→48.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10422 0 179 0 10601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410778
X-RAY DIFFRACTIONf_angle_d0.88414622
X-RAY DIFFRACTIONf_chiral_restr0.0541673
X-RAY DIFFRACTIONf_plane_restr0.0031855
X-RAY DIFFRACTIONf_dihedral_angle_d16.4483793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4807-3.56770.38471440.31582534267896
3.5677-3.66410.29191450.266326332778100
3.6641-3.77190.28871360.240126692805100
3.7719-3.89360.29531470.242826392786100
3.8936-4.03270.2731380.22582637277599
4.0327-4.19410.29281480.207926632811100
4.1941-4.38480.26681450.20392646279199
4.3848-4.61580.21161440.18222658280299
4.6158-4.90480.22521340.17672693282799
4.9048-5.2830.26851220.18612705282799
5.283-5.81390.23981300.21052689281999
5.8139-6.65330.27191640.23042675283998
6.6533-8.37520.22051460.19752714286097
8.3752-48.0490.20931190.19162628274789

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