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- PDB-9lfc: Cryo-EM structure of human bradykinin receptor B1R bound to antag... -

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Basic information

Entry
Database: PDB / ID: 9lfc
TitleCryo-EM structure of human bradykinin receptor B1R bound to antagonist R715
Components
  • B1 bradykinin receptor,Kappa-type opioid receptor
  • Nanobody 6
  • R715
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / bradykinin receptor / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / G protein-coupled opioid receptor signaling pathway ...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 / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / positive regulation of potassium ion transmembrane transport / receptor serine/threonine kinase binding / maternal behavior / positive regulation of p38MAPK cascade / positive regulation of leukocyte migration / neuropeptide binding / sensory perception / eating behavior / response to mechanical stimulus / estrous cycle / conditioned place preference / MECP2 regulates neuronal receptors and channels / negative regulation of blood pressure / peptide binding / behavioral response to cocaine / T-tubule / sensory perception of pain / axon terminus / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / response to nicotine / neuropeptide signaling pathway / cellular response to glucose stimulus / locomotory behavior / negative regulation of cell growth / response to insulin / response to estrogen / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell migration / synaptic vesicle membrane / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / presynaptic membrane / response to lipopolysaccharide / 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 / neuron projection / immune response / G protein-coupled receptor signaling pathway / inflammatory response / dendrite / endoplasmic reticulum / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Bradykinin receptor B1 / 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
Kappa-type opioid receptor / B1 bradykinin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
synthetic construct (others)
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 B1R bound to antagonist R715
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: B1 bradykinin receptor,Kappa-type opioid receptor
C: Nanobody 6
B: R715


Theoretical massNumber of molelcules
Total (without water)58,9013
Polymers58,9013
Non-polymers00
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 B1 bradykinin receptor,Kappa-type opioid receptor / B1R / BK-1 receptor / K-OR-1 / KOR-1


Mass: 38958.918 Da / Num. of mol.: 1 / Mutation: S124K/S132C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDKRB1, BRADYB1, OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P46663, UniProt: P41145
#2: Antibody Nanobody 6


Mass: 18816.033 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: Protein/peptide R715


Mass: 1126.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PubChem ID 5311397 / Source: (synth.) synthetic construct (others)
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 B1R with kappa-type opioid receptor ICL3 in complex with Nb6, R715
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.057 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: 1500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k 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: 232403 / 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_d0.0043216
ELECTRON MICROSCOPYf_angle_d0.7194393
ELECTRON MICROSCOPYf_dihedral_angle_d5.56481
ELECTRON MICROSCOPYf_chiral_restr0.045507
ELECTRON MICROSCOPYf_plane_restr0.004549

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