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- PDB-9lfd: Cryo-EM structure of human bradykinin receptor B2R bound to antag... -

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Basic information

Entry
Database: PDB / ID: 9lfd
TitleCryo-EM structure of human bradykinin receptor B2R bound to antagonist Win64338
Components
  • B2 bradykinin receptor,Kappa-type opioid receptor
  • Nanobody 6
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / bradykinin receptor / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / bradykinin receptor activity / response to acrylamide / dynorphin receptor activity / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / negative regulation of luteinizing hormone secretion ...negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / bradykinin receptor activity / response to acrylamide / dynorphin receptor activity / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / G protein-coupled opioid receptor signaling pathway / vasoconstriction / type 1 angiotensin receptor binding / positive regulation of dopamine secretion / positive regulation of potassium ion transmembrane transport / receptor serine/threonine kinase binding / regulation of vascular permeability / maternal behavior / positive regulation of p38MAPK cascade / neuropeptide binding / arachidonate secretion / blood circulation / sensory perception / eating behavior / smooth muscle contraction / regulation of vasoconstriction / estrous cycle / conditioned place preference / MECP2 regulates neuronal receptors and channels / response to salt stress / behavioral response to cocaine / T-tubule / sensory perception of pain / cell surface receptor protein tyrosine kinase signaling pathway / axon terminus / Peptide ligand-binding receptors / sarcoplasmic reticulum / response to nicotine / neuropeptide signaling pathway / cellular response to glucose stimulus / locomotory behavior / response to insulin / response to estrogen / vasodilation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / synaptic vesicle membrane / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / protease binding / presynaptic membrane / defense response to virus / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / response to ethanol / perikaryon / postsynaptic membrane / cell surface receptor signaling pathway / endosome / neuron projection / immune response / G protein-coupled receptor signaling pathway / protein heterodimerization activity / inflammatory response / dendrite / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Bradykinin receptor B2 / Bradykinin receptor family / Kappa opioid receptor / Opioid receptor / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / B2 bradykinin receptor / Kappa-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXia, M. / Zhang, H.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)81722044 China
National Natural Science Foundation of China (NSFC)91753115 China
National Natural Science Foundation of China (NSFC)21778049 China
National Natural Science Foundation of China (NSFC)81861148018 China
Ministry of Science and Technology (MoST, China)2018ZX09711002 China
CitationJournal: To Be Published
Title: Cryo-EM structure of human bradykinin receptor B2R bound to antagonist Win64338
Authors: Xia, M. / Zhang, H.
History
DepositionJan 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B2 bradykinin receptor,Kappa-type opioid receptor
C: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0193
Polymers56,3072
Non-polymers7121
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein B2 bradykinin receptor,Kappa-type opioid receptor / B2R / BK-2 receptor / K-OR-1 / KOR-1


Mass: 41577.094 Da / Num. of mol.: 1 / Mutation: S144K/C146W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDKRB2, BKR2, OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30411, UniProt: P41145
#2: Antibody Nanobody 6


Mass: 14730.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical ChemComp-A1EJK / Win64338


Mass: 712.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H68N4OP / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

ComponentName: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in complex with Nb6, Win64338
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.056 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2cryoSPARCparticle selection
9PHENIXmodel refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252676 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022927
ELECTRON MICROSCOPYf_angle_d0.5013984
ELECTRON MICROSCOPYf_dihedral_angle_d3.985423
ELECTRON MICROSCOPYf_chiral_restr0.035481
ELECTRON MICROSCOPYf_plane_restr0.003472

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