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- PDB-7f2o: Cryo-EM structure of the type 2 bradykinin receptor in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7f2o
TitleCryo-EM structure of the type 2 bradykinin receptor in complex with the bradykinin and an Gq protein
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE-ARG
  • B2 bradykinin receptor
  • G subunit q (Gi1-Gq chimeric)
  • single Fab chain (svFv16)
KeywordsMEMBRANE PROTEIN / GPCR / Complex
Function / homology
Function and homology information


negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / bradykinin receptor activity / regulation of vascular permeability / phosphatidylinositol phospholipase C activity / vasoconstriction / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste ...negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / bradykinin receptor activity / regulation of vascular permeability / phosphatidylinositol phospholipase C activity / vasoconstriction / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / type 1 angiotensin receptor binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / blood circulation / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / 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 / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / alkylglycerophosphoethanolamine phosphodiesterase activity / 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 / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / arachidonic acid secretion / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of peptidyl-serine phosphorylation / plasma membrane => GO:0005886 / smooth muscle contraction / regulation of vasoconstriction / photoreceptor outer segment / cardiac muscle cell apoptotic process / cell surface receptor protein tyrosine kinase signaling pathway / response to salt stress / photoreceptor inner segment / Peptide ligand-binding receptors / G protein-coupled receptor activity / cellular response to catecholamine stimulus / sensory perception of taste / adenylate cyclase-activating dopamine receptor signaling pathway / vasodilation / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cell body / cellular response to hypoxia / G alpha (q) signalling events / protease binding / cell population proliferation / cell surface receptor signaling pathway / endosome / inflammatory response / G protein-coupled receptor signaling pathway / protein heterodimerization activity / intracellular membrane-bounded organelle / GTPase activity / dendrite / protein-containing complex binding / Golgi apparatus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Bradykinin receptor B2 / Bradykinin receptor family / 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 ...Bradykinin receptor B2 / Bradykinin receptor family / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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
Similarity search - Domain/homology
B2 bradykinin receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
synthetic construct (others)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYin, Y. / Jiang, Y.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507002 China
National Natural Science Foundation of China (NSFC)31770796 China
National Natural Science Foundation of China (NSFC)81872915 China
National Natural Science Foundation of China (NSFC)82073904 China
National Natural Science Foundation of China (NSFC)81773792 China
National Natural Science Foundation of China (NSFC)81973373 China
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Molecular basis for kinin selectivity and activation of the human bradykinin receptors.
Authors: Yu-Ling Yin / Chenyu Ye / Fulai Zhou / Jia Wang / Dehua Yang / Wanchao Yin / Ming-Wei Wang / H Eric Xu / Yi Jiang /
Abstract: Bradykinin and kallidin are endogenous kinin peptide hormones that belong to the kallikrein-kinin system and are essential to the regulation of blood pressure, inflammation, coagulation and pain ...Bradykinin and kallidin are endogenous kinin peptide hormones that belong to the kallikrein-kinin system and are essential to the regulation of blood pressure, inflammation, coagulation and pain control. Des-Arg-kallidin, the carboxy-terminal des-Arg metabolite of kallidin, and bradykinin selectively activate two G protein-coupled receptors, type 1 and type 2 bradykinin receptors (B1R and B2R), respectively. The hyperactivation of bradykinin receptors, termed 'bradykinin storm', is associated with pulmonary edema in COVID-19 patients, suggesting that bradykinin receptors are important targets for COVID-19 intervention. Here we report two G protein-coupled complex structures of human B1R and B2R bound to des-Arg-kallidin and bradykinin, respectively. Combined with functional analysis, our structures reveal the mechanism of ligand selectivity and specific activation of the bradykinin receptor. These findings also provide a framework for guiding drug design targeting bradykinin receptors for the treatment of inflammation, cardiovascular disorders and COVID-19.
History
DepositionJun 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: G subunit q (Gi1-Gq chimeric)
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
D: ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE-ARG
R: B2 bradykinin receptor
S: single Fab chain (svFv16)
Y: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2


Theoretical massNumber of molelcules
Total (without water)185,2496
Polymers185,2496
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13610 Å2
ΔGint-75 kcal/mol
Surface area46780 Å2

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Components

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Protein , 2 types, 2 molecules AR

#1: Protein G subunit q (Gi1-Gq chimeric)


Mass: 41724.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein B2 bradykinin receptor / B2R / BK-2 receptor


Mass: 67152.914 Da / Num. of mol.: 1 / Mutation: C146W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDKRB2, BKR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30411

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules BY

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


Mass: 41055.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54311
#6: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212

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Protein/peptide / Antibody , 2 types, 2 molecules DS

#3: Protein/peptide ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE-ARG


Mass: 1062.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Antibody single Fab chain (svFv16)


Mass: 26392.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of the type 2 bradykinin receptor in complex with the bradykinin and an Gq proteinCOMPLEXall0MULTIPLE SOURCES
2G subunit q (Gi2-mini-Gq chimeric)COMPLEX#11RECOMBINANT
3Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1COMPLEX#21RECOMBINANT
4ARG-PRO-PRO-GLY-PHE-SER-PRO-PHE-ARGCOMPLEX#31SYNTHETIC
5Type 2 bradykinin receptorCOMPLEX#41RECOMBINANT
6single Fab chain (svFv16)COMPLEX#51RECOMBINANT
7Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2COMPLEX#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
44Rattus norvegicus (Norway rat)10116
55Homo sapiens (human)9606
66Bos taurus (cattle)9913
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
44Spodoptera frugiperda (fall armyworm)7108
55Spodoptera frugiperda (fall armyworm)7108
66Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Film or detector model: OTHER

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 664416 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029254
ELECTRON MICROSCOPYf_angle_d0.5512562
ELECTRON MICROSCOPYf_dihedral_angle_d21.8023308
ELECTRON MICROSCOPYf_chiral_restr0.0421435
ELECTRON MICROSCOPYf_plane_restr0.0051580

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