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- PDB-8qeh: Crystal structure of the G11 protein heterotrimer bound to FR9003... -

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Basic information

Entry
Database: PDB / ID: 8qeh
TitleCrystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
Components(Guanine nucleotide-binding protein ...) x 3
KeywordsSIGNALING PROTEIN / G protein / FR900359 / cell signaling / GNA11 / GNB1 / GNG2 / G alpha 11
Function / homology
Function and homology information


regulation of melanocyte differentiation / : / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / developmental pigmentation / cellular response to pH / PLC beta mediated events / entrainment of circadian clock ...regulation of melanocyte differentiation / : / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / developmental pigmentation / cellular response to pH / PLC beta mediated events / entrainment of circadian clock / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / phototransduction, visible light / ligand-gated ion channel signaling pathway / action potential / photoreceptor outer segment / enzyme regulator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / skeletal system development / G protein-coupled receptor binding / positive regulation of insulin secretion / regulation of blood pressure / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / G protein activity / heart development / GTPase binding / Ca2+ pathway / retina development in camera-type eye / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
G-protein alpha subunit, group Q / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily ...G-protein alpha subunit, group Q / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ALANINE / N-METHYL-ALPHA-BETA-DEHYDROALANINE / GUANOSINE-5'-DIPHOSPHATE / (2R)-2-hydroxy-3-phenylpropanoic acid / (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid / N-methyl-L-alanine / N,O-dimethyl-L-threonine / PROPANOIC ACID / : / Guanine nucleotide-binding protein subunit alpha-11 ...ALANINE / N-METHYL-ALPHA-BETA-DEHYDROALANINE / GUANOSINE-5'-DIPHOSPHATE / (2R)-2-hydroxy-3-phenylpropanoic acid / (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid / N-methyl-L-alanine / N,O-dimethyl-L-threonine / PROPANOIC ACID / : / Guanine nucleotide-binding protein subunit alpha-11 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMuehle, J. / Rodrigues, M.J. / Guixa-Gonzalez, R. / Deupi, X. / Schertler, G.F.X.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)273251628 Germany
CitationJournal: To Be Published
Title: Structure of the heterotrimeric G11 protein bound to the cyclic depsipeptides FR900359 and YM-254890
Authors: Muehle, J. / Schertler, G.F.X.
History
DepositionAug 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein subunit alpha-11
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,03325
Polymers86,6563
Non-polymers2,37722
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.644, 95.813, 126.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#1: Protein Guanine nucleotide-binding protein subunit alpha-11 / G alpha-11 / G-protein subunit alpha-11 / Guanine nucleotide-binding protein G(y) subunit alpha


Mass: 41139.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNA11, GA11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29992
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1


Mass: 37671.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7845.078 Da / Num. of mol.: 1 / Mutation: C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768

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Non-polymers , 14 types, 782 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DAM / N-METHYL-ALPHA-BETA-DEHYDROALANINE


Type: peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-HF2 / (2R)-2-hydroxy-3-phenylpropanoic acid


Type: peptide-like / Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-UDL / (2~{S},3~{R})-2-acetamido-4-methyl-3-oxidanyl-pentanoic acid


Mass: 189.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-OTH / N,O-dimethyl-L-threonine


Type: L-peptide linking / Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-HL2 / (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid / BETA-HYDROXYLEUCINE


Type: L-peptide linking / Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-MAA / N-methyl-L-alanine


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5% n-octyl-beta-D-Glucoside and 10 mM Zinc sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→126.8 Å / Num. obs: 163494 / % possible obs: 100 % / Redundancy: 44 % / CC1/2: 1 / Net I/σ(I): 16.5
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 46.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 8016 / CC1/2: 0.309 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→63.113 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.124 / SU B: 3.456 / SU ML: 0.054 / Average fsc free: 0.9661 / Average fsc work: 0.9788 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 7962 4.873 %RANDOM
Rwork0.1399 155413 --
all0.142 ---
obs-163375 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.784 Å2
Baniso -1Baniso -2Baniso -3
1-2.511 Å20 Å2-0 Å2
2---3.419 Å20 Å2
3---0.908 Å2
Refinement stepCycle: LAST / Resolution: 1.43→63.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 113 760 6628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165732
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6488610
X-RAY DIFFRACTIONr_angle_other_deg0.5181.56713337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.09553
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.38751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.088101065
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.47610281
X-RAY DIFFRACTIONr_chiral_restr0.0710.2970
X-RAY DIFFRACTIONr_chiral_restr_other0.090.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021310
X-RAY DIFFRACTIONr_nbd_refined0.3010.21162
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.25397
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2566
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.214
X-RAY DIFFRACTIONr_nbd_other0.1940.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0710.21
X-RAY DIFFRACTIONr_mcbond_it2.6082.443162
X-RAY DIFFRACTIONr_mcbond_other2.6092.5113163
X-RAY DIFFRACTIONr_mcangle_it3.4183.6584005
X-RAY DIFFRACTIONr_mcangle_other3.4183.6954005
X-RAY DIFFRACTIONr_scbond_it3.4172.8193174
X-RAY DIFFRACTIONr_scbond_other3.4162.8183175
X-RAY DIFFRACTIONr_scangle_it4.3184.0824605
X-RAY DIFFRACTIONr_scangle_other4.3174.0824606
X-RAY DIFFRACTIONr_lrange_it4.74136.3787316
X-RAY DIFFRACTIONr_lrange_other4.74136.3787317
X-RAY DIFFRACTIONr_rigid_bond_restr3.488312063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.43-1.4670.3385770.33113640.33119510.9110.92699.91630.327
1.467-1.5070.3115630.298111090.298116730.9250.94599.99140.29
1.507-1.5510.3275780.274107430.277113250.9270.95699.96470.259
1.551-1.5990.2595100.218105350.22110460.9590.97399.99090.198
1.599-1.6510.2355560.188101660.19107220.9670.9811000.162
1.651-1.7090.2115110.16698380.168103490.9720.9851000.138
1.709-1.7730.2024760.1495240.143100010.9770.9999.990.113
1.773-1.8460.184920.12391310.12696240.980.99299.98960.097
1.846-1.9280.1844480.11888070.12192550.9810.9931000.094
1.928-2.0220.1614260.10284180.10488470.9870.99599.96610.082
2.022-2.1310.1624140.10680390.10984530.9840.9941000.089
2.131-2.260.1584000.175870.10379870.9850.9951000.085
2.26-2.4160.1613510.09971710.10275220.9860.9951000.085
2.416-2.6090.1653440.10767050.1170490.9830.9941000.094
2.609-2.8580.1583040.11361520.11564560.9850.9921000.102
2.858-3.1940.1682650.1256350.12259000.9810.9911000.113
3.194-3.6870.1772510.13849650.1452160.9810.991000.135
3.687-4.5120.1432370.12342230.12444620.9890.99199.95520.125
4.512-6.3640.1831690.15833430.15935120.9820.9871000.163
6.364-63.1130.175900.20519590.20420500.9850.96699.95120.205

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