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- PDB-4g5q: Structure of LGN GL4/Galphai1 complex -

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Basic information

Entry
Database: PDB / ID: 4g5q
TitleStructure of LGN GL4/Galphai1 complex
Components
  • G-protein-signaling modulator 2
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsCELL CYCLE/SIGNALING PROTEIN / Galphai / 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 / G alpha (i) signalling events / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding ...lateral cell cortex / cell cortex region / maintenance of centrosome location / G alpha (i) signalling events / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / regulation of mitotic spindle organization / mitotic spindle organization / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / centriolar satellite / G-protein beta/gamma-subunit complex binding / ADP signalling through P2Y purinoceptor 12 / GDP binding / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / heterotrimeric G-protein complex / G protein activity / midbody / cell cortex / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Extra-nuclear estrogen signaling / postsynaptic density / ciliary basal body / G protein-coupled receptor signaling pathway / protein domain specific binding / lysosomal membrane / cell division / nucleotide binding / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / Golgi apparatus / protein-containing complex / extracellular exosome / nucleoplasm / identical protein 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 ...: / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / G-protein alpha subunit, group I / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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-1 / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJia, M. / Li, J. / Zhu, J. / Wen, W. / Zhang, M. / Wang, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structures of the scaffolding protein LGN reveal the general mechanism by which GoLoco binding motifs inhibit the release of GDP from G alpha i.
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
Revision 1.2Mar 5, 2025Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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) subunit alpha-1
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
D: Guanine nucleotide-binding protein G(i) subunit alpha-1
E: G-protein-signaling modulator 2
F: G-protein-signaling modulator 2
G: G-protein-signaling modulator 2
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,50433
Polymers163,3308
Non-polymers4,17425
Water63135
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
E: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6607
Polymers40,8322
Non-polymers8275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-64 kcal/mol
Surface area16280 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
F: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0449
Polymers40,8322
Non-polymers1,2127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-59 kcal/mol
Surface area15660 Å2
MethodPISA
3
C: Guanine nucleotide-binding protein G(i) subunit alpha-1
G: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8528
Polymers40,8322
Non-polymers1,0206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-61 kcal/mol
Surface area16700 Å2
MethodPISA
4
D: Guanine nucleotide-binding protein G(i) subunit alpha-1
H: G-protein-signaling modulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9489
Polymers40,8322
Non-polymers1,1167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-67 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.376, 207.376, 236.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A32 - 349
221B32 - 349
112A31 - 350
222C31 - 350
113A31 - 349
223D31 - 349
114B33 - 349
224C33 - 349
115B33 - 348
225D33 - 348
116C31 - 354
226D31 - 354
117E499 - 518
227F499 - 518
118E499 - 518
228G499 - 518
119E499 - 518
229H499 - 518
1110F498 - 518
2210G498 - 518
1111F498 - 519
2211H498 - 519
1112G498 - 518
2212H498 - 518

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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


Mass: 37732.918 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: GNAI1, GNAI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63096
#2: Protein/peptide
G-protein-signaling modulator 2 / LGN / Pins homolog


Mass: 3099.544 Da / Num. of mol.: 4 / Fragment: GoLoco 4 (UNP RESIDUES 628-652) / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8VDU0

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Non-polymers , 4 types, 60 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-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


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 4.5 Å3/Da / Density % sol: 72.65 % / Mosaicity: 0.173 °
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: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 66971 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.096 / Χ2: 1.25 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.959.70.73533011.11100
2.95-39.70.62432881.1181100
3-3.069.70.51932781.1231100
3.06-3.129.70.42632921.151100
3.12-3.199.70.36433161.1461100
3.19-3.279.70.30832871.1631100
3.27-3.359.70.25433171.21100
3.35-3.449.60.20132961.2831100
3.44-3.549.60.16933201.3341100
3.54-3.659.60.14432981.3931100
3.65-3.789.30.13333321.4391100
3.78-3.949.20.11433211.421100
3.94-4.119.50.07933181.1961100
4.11-4.339.50.07133591.2241100
4.33-4.69.50.06733551.361100
4.6-4.969.20.0733581.431100
4.96-5.4690.07133961.3461100
5.46-6.248.90.07534081.3731100
6.24-7.868.90.04934611.1661100
7.86-508.80.02336701.061199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.211 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 3385 5.1 %RANDOM
Rwork0.2073 ---
obs0.209 66859 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.68 Å2 / Biso mean: 65.7073 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10914 0 249 35 11198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211346
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.97315327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57251360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86424.393535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.285152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5171565
X-RAY DIFFRACTIONr_chiral_restr0.1490.21723
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028366
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A4150.16
12B4150.16
21A4080.17
22C4080.17
31A3930.18
32D3930.18
41B4050.19
42C4050.19
51B3960.18
52D3960.18
61C4020.17
62D4020.17
71E190.16
72F190.16
81E180.16
82G180.16
91E160.26
92H160.26
101F200.21
102G200.21
111F160.25
112H160.25
121G170.28
122H170.28
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 237 -
Rwork0.317 4262 -
all-4499 -
obs--99.73 %

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