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- PDB-6qnk: Antibody FAB fragment targeting Gi protein heterotrimer -

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Basic information

Entry
Database: PDB / ID: 6qnk
TitleAntibody FAB fragment targeting Gi protein heterotrimer
Components
  • FAB heavy chainFragment antigen-binding
  • FAB light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Antibody FAB fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / D-MALATE / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTsai, C.-J. / Muehle, J. / Pamula, F. / Dawson, R.J.P. / Maeda, S. / Deupi, X. / Schertler, G.F.X.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_153145 Switzerland
Swiss National Science Foundation310030B_173335 Switzerland
Swiss National Science Foundation160805 Switzerland
Swiss Nanoscience Institute A13.12 NanoGhip Switzerland
CitationJournal: Elife / Year: 2019
Title: Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit.
Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / ...Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / Xavier Deupi / Henning Stahlberg / Gebhard Schertler /
Abstract: One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently ...One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway.
History
DepositionFeb 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB light chain
B: FAB heavy chain
C: FAB light chain
D: FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,81325
Polymers110,6494
Non-polymers2,16421
Water7,026390
1
A: FAB light chain
B: FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,62815
Polymers55,3242
Non-polymers1,30313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint14 kcal/mol
Surface area19180 Å2
MethodPISA
2
C: FAB light chain
D: FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18510
Polymers55,3242
Non-polymers8618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-10 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.940, 68.080, 133.670
Angle α, β, γ (deg.)90.00, 127.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-499-

HOH

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody FAB light chain / Fragment antigen-binding


Mass: 26309.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Fragment: House mouse / Production host: hybrid (others)
#2: Antibody FAB heavy chain / Fragment antigen-binding


Mass: 29014.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Fragment: House mouse / Production host: hybrid (others)

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Non-polymers , 5 types, 411 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H6O5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 3.24 Å3/Da / Density % sol: 62.07 % / Description: Rhombus plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5 M (pH 7.5) malic acid, 7 % (v/v) lauryldimethylamine N-oxide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection

Entry-ID: 6QNK / Redundancy: 3.5 %

Resolution (Å)Num. obs% possible obs (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.9-47.729481197.90.9980.090.0570.10717.2
1.9-47.729508198.10.0830.0520.09827.6
1.9-47.649513398.60.9980.0830.0520.09837.6
1.9-47.649513198.60.9980.0840.0520.09947.4
1.9-47.649511398.60.9990.0780.0480.09258
1.9-47.649498198.40.9980.0850.0530.10167.2
Reflection shell

Resolution: 1.9→1.97 Å

Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
3.67.9610.194270.044.8639.351198.1
3.57.5110.194280.034.5738.815298.1
3.64.140.294760.1062.5184.858399.3
3.65.5780.294360.0523.3946.545498.8
3.66.3630.194320.0463.877.465598.8
3.68.4360.193830.0225.1319.896698.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(1.13_2998-000)model building
PHENIX(1.13_2998-000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1200000000 / Resolution: 1.9→45.92 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.27
RfactorNum. reflection% reflection
Rfree0.2122 1989 2.94 %
Rwork0.1795 --
obs0.1805 67745 70.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 143 390 7190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057098
X-RAY DIFFRACTIONf_angle_d0.789642
X-RAY DIFFRACTIONf_dihedral_angle_d4.9315626
X-RAY DIFFRACTIONf_chiral_restr0.0491071
X-RAY DIFFRACTIONf_plane_restr0.0051223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94770.3405240.312864X-RAY DIFFRACTION13
1.9477-2.00030.2733380.261138X-RAY DIFFRACTION17
2.0003-2.05920.2984490.2731520X-RAY DIFFRACTION23
2.0592-2.12570.2468670.25482113X-RAY DIFFRACTION32
2.1257-2.20160.2933800.25292926X-RAY DIFFRACTION44
2.2016-2.28980.26491420.2454561X-RAY DIFFRACTION69
2.2898-2.3940.30851850.25986363X-RAY DIFFRACTION96
2.394-2.52020.26672050.25396500X-RAY DIFFRACTION98
2.5202-2.67810.25911900.24016497X-RAY DIFFRACTION97
2.6781-2.88480.25492020.22576621X-RAY DIFFRACTION100
2.8848-3.17510.25242050.21186631X-RAY DIFFRACTION100
3.1751-3.63430.21951950.17466642X-RAY DIFFRACTION100
3.6343-4.57820.17322010.13486701X-RAY DIFFRACTION100
4.5782-45.93350.15662060.13416679X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1599-0.54790.73621.83230.26051.98020.41261.4486-0.029-0.185-0.45590.0423-0.2559-0.25790.04240.3661-0.0631-0.01150.78610.01030.262465.000751.69399.1423
24.3683-1.9266-0.14171.85610.12843.6866-0.05061.0597-0.7744-0.069-0.2350.19190.2241-0.26140.14220.3087-0.17360.01780.5228-0.10430.310565.094944.931914.2352
33.0871-0.7935-0.64271.5805-0.80280.791-0.14040.5615-0.17410.08650.030.1289-0.4028-0.33920.09760.2733-0.0796-0.03540.2827-0.04380.283937.826754.275331.824
42.9795-0.1035-1.18042.16781.96854.9476-0.02180.55660.1899-0.308-0.14440.2586-0.8201-0.63580.14510.43970.0336-0.06560.37880.01780.32234.53760.721830.3244
54.6674-0.7451-0.8952.74050.95632.3194-0.0907-0.2699-0.08340.5343-0.0018-0.29020.15680.1320.07880.3222-0.0933-0.06230.30040.08790.221376.226949.401932.2566
63.5502-0.3131-1.8020.98540.53522.1816-0.2020.1279-0.08690.07970.10180.0287-0.04820.08660.05830.3323-0.0808-0.01340.23510.05650.232561.124751.124633.3445
75.20172.21721.38852.81890.69372.2179-0.14860.3383-0.202-0.1041-0.01260.16250.29720.10440.14050.4325-0.02810.08030.22-0.02060.281943.680850.050341.6556
83.62260.80070.39661.02930.29845.0449-0.25970.0815-0.11470.0277-0.12390.08910.3396-0.27410.35120.3967-0.03960.07220.157-0.04860.339840.111848.637642.0806
92.3881-0.2528-0.88991.9950.24612.45240.02111.3653-0.2805-0.1002-0.0357-0.17990.18710.15010.01170.4566-0.17980.00640.81890.02240.301624.4622.89468.9884
103.7025-0.47591.23761.1937-0.61011.6467-0.3330.97930.6785-0.23280.0753-0.01160.04840.07780.20090.3856-0.20170.00830.48540.11870.286431.345827.507718.4224
113.3729-0.29761.36112.3645-1.95015.65670.00010.5506-0.0429-0.3545-0.1426-0.23320.87310.73050.12020.45270.01620.06990.38850.00260.345854.568914.609730.3439
125.75810.73470.33033.0792-0.60642.8074-0.0318-0.07280.72450.2730.12880.4382-0.2952-0.0096-0.06060.2363-0.06790.03880.2511-0.00130.290213.859726.551830.3465
133.29410.88521.90841.9119-1.38293.7574-0.1352-0.0882-0.4631-0.0162-0.0747-0.41070.00230.27630.15470.37360.0077-0.01260.19-0.10770.313545.179420.184242.5206
143.81630.8292-1.01261.1194-0.86584.5008-0.25050.03320.1761-0.0563-0.0777-0.133-0.34310.12830.29710.3509-0.0453-0.06730.16160.02190.341347.715826.343341.9349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 237 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 102 )
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 240 )
9X-RAY DIFFRACTION9chain 'C' and (resid 21 through 57 )
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 153 )
11X-RAY DIFFRACTION11chain 'C' and (resid 154 through 237 )
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 133 )
13X-RAY DIFFRACTION13chain 'D' and (resid 134 through 161 )
14X-RAY DIFFRACTION14chain 'D' and (resid 162 through 240 )

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