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- PDB-6b20: Crystal structure of a complex between G protein beta gamma dimer... -

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Basic information

Entry
Database: PDB / ID: 6b20
TitleCrystal structure of a complex between G protein beta gamma dimer and an inhibitory Nanobody regulator
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • Nanobody against G protein beta gamma dimer
KeywordsSIGNALING PROTEIN / Beta propeller / G protein / G protein coupled receptor-signaling
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / protein localization / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / protein-containing complex binding / membrane / cytoplasm
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesBos taurus (cattle)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGulati, S. / Kiser, P.D. / Palczewski, K.
CitationJournal: Nat Commun / Year: 2018
Title: Targeting G protein-coupled receptor signaling at the G protein level with a selective nanobody inhibitor.
Authors: Gulati, S. / Jin, H. / Masuho, I. / Orban, T. / Cai, Y. / Pardon, E. / Martemyanov, K.A. / Kiser, P.D. / Stewart, P.L. / Ford, C.P. / Steyaert, J. / Palczewski, K.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.2Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(T) subunit gamma-T1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
D: Guanine nucleotide-binding protein G(T) subunit gamma-T1
E: Nanobody against G protein beta gamma dimer
F: Nanobody against G protein beta gamma dimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,23218
Polymers113,1976
Non-polymers3512
Water7,134396
1
A: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(T) subunit gamma-T1
F: Nanobody against G protein beta gamma dimer


Theoretical massNumber of molelcules
Total (without water)56,5989
Polymers56,5983
Non-polymers06
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-44 kcal/mol
Surface area21570 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
D: Guanine nucleotide-binding protein G(T) subunit gamma-T1
E: Nanobody against G protein beta gamma dimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6349
Polymers56,5983
Non-polymers356
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-54 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.660, 77.230, 101.660
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASNASNAA3 - 3401 - 338
21GLUGLUASNASNBC3 - 3401 - 338
12GLUGLUPHEPHECB11 - 645 - 58
22GLUGLUPHEPHEDD11 - 645 - 58
13GLNGLNSERSEREE1 - 1141 - 114
23GLNGLNSERSERFF1 - 1141 - 114

NCS ensembles :
ID
1
2
3

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Components

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Guanine nucleotide-binding protein ... , 2 types, 4 molecules ABCD

#1: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37212.680 Da / Num. of mol.: 2 / Mutation: V71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P62871
#2: Protein Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Transducin gamma chain


Mass: 7130.106 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: P02698

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Antibody , 1 types, 2 molecules EF

#3: Antibody Nanobody against G protein beta gamma dimer


Mass: 12255.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / Variant (production host): (Su-)

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Non-polymers , 3 types, 408 molecules

#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 25-30% (w/v) PEG 3350 in 0.1-0.2 M Bis-Tris-HCl, pH 5.5-5.7, and 0.2-0.3 M MgCl2
PH range: 5.5-5.7

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Data collection

DiffractionMean temperature: 100.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→47.82 Å / Num. obs: 42434 / % possible obs: 99.6 % / Redundancy: 4.31 % / CC1/2: 0.991 / Rpim(I) all: 0.22 / Net I/σ(I): 6.28
Reflection shellResolution: 2.34→2.4 Å / Redundancy: 4.43 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 3268 / CC1/2: 0.507 / Rpim(I) all: 1.77 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A0R

1a0r


Resolution: 2.34→47.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.768 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24906 2234 5 %RANDOM
Rwork0.20034 ---
obs0.20283 42434 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-1.95 Å2
2--3.38 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 2.34→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 12 396 8280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198031
X-RAY DIFFRACTIONr_bond_other_d0.0020.027281
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.94310864
X-RAY DIFFRACTIONr_angle_other_deg0.988316872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10751025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31223.862378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.897151377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7181568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021693
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6375.0864082
X-RAY DIFFRACTIONr_mcbond_other3.6355.0854081
X-RAY DIFFRACTIONr_mcangle_it5.6357.6165095
X-RAY DIFFRACTIONr_mcangle_other5.6347.6175096
X-RAY DIFFRACTIONr_scbond_it3.8695.523949
X-RAY DIFFRACTIONr_scbond_other3.8695.523949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1058.095764
X-RAY DIFFRACTIONr_long_range_B_refined9.9794.835620
X-RAY DIFFRACTIONr_long_range_B_other9.96694.79935607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A215080.07
12B215080.07
21C30000.1
22D30000.1
31E68900.04
32F68900.04
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 163 -
Rwork0.363 3096 -
obs--100 %

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