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- PDB-6crk: Heterotrimeric G-protein in complex with an antibody fragment -

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Basic information

Entry
Database: PDB / ID: 6crk
TitleHeterotrimeric G-protein in complex with an antibody fragment
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • single-chain FvSingle-chain variable fragment
KeywordsSIGNALING PROTEIN / Heterotrimeric G-protein antibody fragment
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 / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to peptide hormone / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Adrenaline,noradrenaline inhibits insulin secretion / photoreceptor disc membrane / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / synapse / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / G-protein alpha subunit, group I / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / G-protein alpha subunit, group I / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Few Secondary Structures / Irregular / G-protein beta WD-40 repeat / WD40 repeat, conserved site / P-loop containing nucleotide triphosphate hydrolases / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / GUANOSINE-5'-DIPHOSPHATE / 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 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMaeda, S. / Dawson, R. / Kobilka, B.
CitationJournal: Nat Commun / Year: 2018
Title: Development of an antibody fragment that stabilizes GPCR/G-protein complexes.
Authors: Maeda, S. / Koehl, A. / Matile, H. / Hu, H. / Hilger, D. / Schertler, G.F.X. / Manglik, A. / Skiniotis, G. / Dawson, R.J.P. / Kobilka, B.K.
History
DepositionMar 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H: single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4286
Polymers113,7964
Non-polymers6322
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-63 kcal/mol
Surface area40550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.514, 104.739, 211.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

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Components

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

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


Mass: 40438.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63096
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37728.152 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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Antibody , 1 types, 1 molecules H

#4: Antibody single-chain Fv / Single-chain variable fragment


Mass: 27784.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)

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Non-polymers , 3 types, 629 molecules

#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 8000, 0.1M Sodium citrate pH 5.0, 1mM MgCl2, 10uM GDP, 100uM TCEP, 1mM aluminium chloride, 10mM sodium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→39.26 Å / Num. obs: 88263 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 37.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Net I/σ(I): 13.5 / Num. measured all: 409653 / Scaling rejects: 72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.044.71.0842111944620.4740.5561.2251.599.5
10.77-39.264.30.02627906510.9940.0140.0347.796.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP2 and 4NKD

1gp2

4nkd


Resolution: 2→39.26 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33
RfactorNum. reflection% reflection
Rfree0.2097 4410 5 %
Rwork0.1746 --
obs-88191 99.18 %
Displacement parametersBiso max: 149.13 Å2 / Biso mean: 47.33 Å2 / Biso min: 20.15 Å2
Refinement stepCycle: final / Resolution: 2→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 41 628 8173
Biso mean--31.55 51.44 -
Num. residues----980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.32381440.29382742288699
2.0227-2.04650.32781450.270127472892100
2.0465-2.07150.25521470.257627852932100
2.0715-2.09770.28281460.2427862932100
2.0977-2.12530.2651430.234927142857100
2.1253-2.15440.26831480.23392813296199
2.1544-2.18520.29941460.234127622908100
2.1852-2.21780.28781470.218827922939100
2.2178-2.25250.24041450.213527852930100
2.2525-2.28940.27981430.20732711285499
2.2894-2.32890.26351450.20752740288597
2.3289-2.37120.2291460.199927712917100
2.3712-2.41680.25871470.201528052952100
2.4168-2.46610.27291470.200527752922100
2.4661-2.51980.25841470.200528012948100
2.5198-2.57840.26551460.190827842930100
2.5784-2.64280.22541470.186127992946100
2.6428-2.71430.23021480.18927872935100
2.7143-2.79410.2121440.18682764290898
2.7941-2.88430.2261450.19282742288798
2.8843-2.98730.25631470.185628062953100
2.9873-3.10690.20111490.18592821297099
3.1069-3.24820.21491480.175928242972100
3.2482-3.41940.23881490.176328292978100
3.4194-3.63350.18481480.16172799294799
3.6335-3.91380.16911460.15672780292698
3.9138-4.30720.18211500.1342834298499
4.3072-4.92940.14321510.12292868301999
4.9294-6.20660.19351480.15292834298297
6.2066-39.27110.1851580.17092981313997
Refinement TLS params.Method: refined / Origin x: -65.3868 Å / Origin y: -14.4319 Å / Origin z: -23.5604 Å
111213212223313233
T0.2277 Å2-0.0159 Å20.0171 Å2-0.2396 Å2-0.0343 Å2--0.2008 Å2
L0.4261 °2-0.1205 °2-0.029 °2-0.4139 °2-0.1103 °2--0.223 °2
S0.0084 Å °0.0004 Å °0.0758 Å °-0.0672 Å °-0.0053 Å °-0.026 Å °0.0292 Å °-0.0132 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 355
2X-RAY DIFFRACTION1allB2 - 340
3X-RAY DIFFRACTION1allG5 - 64
4X-RAY DIFFRACTION1allH1 - 248
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allS1 - 628

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