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- EMDB-63044: Cryo-EM structure of human bradykinin receptor B1R bound to antag... -

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Basic information

Entry
Database: EMDB / ID: EMD-63044
TitleCryo-EM structure of human bradykinin receptor B1R bound to antagonist R715
Map data
Sample
  • Complex: bradykinin receptor B1R with kappa-type opioid receptor ICL3 in complex with Nb6, R715
    • Protein or peptide: B1 bradykinin receptor,Kappa-type opioid receptor
    • Protein or peptide: Nanobody 6
  • Protein or peptide: R715
KeywordsGPCR / bradykinin receptor / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXia M / Zhang H
Funding support China, 6 items
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, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63044.png

Downloads & links

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Map

FileDownload / File: emd_63044.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.4002628 - 3.7267718
Average (Standard dev.)-0.0025484925 (±0.056785922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63044_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63044_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : bradykinin receptor B1R with kappa-type opioid receptor ICL3 in c...

EntireName: bradykinin receptor B1R with kappa-type opioid receptor ICL3 in complex with Nb6, R715
Components
  • Complex: bradykinin receptor B1R with kappa-type opioid receptor ICL3 in complex with Nb6, R715
    • Protein or peptide: B1 bradykinin receptor,Kappa-type opioid receptor
    • Protein or peptide: Nanobody 6
  • Protein or peptide: R715

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Supramolecule #1: bradykinin receptor B1R with kappa-type opioid receptor ICL3 in c...

SupramoleculeName: bradykinin receptor B1R with kappa-type opioid receptor ICL3 in complex with Nb6, R715
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57 KDa

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Macromolecule #1: B1 bradykinin receptor,Kappa-type opioid receptor

MacromoleculeName: B1 bradykinin receptor,Kappa-type opioid receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.958918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ASSWPPLELQ SSNQSQLFPQ NATACDNAPE AWDLLHRVLP TFIISICFFG LLGNLFVLLV FLLPRRQLNV AEIYLANLAA SDLVFVLGL PFWAENIWNQ FNWPFGALLC RVINGVIKAN LFIKIFLVVA ICQDRYRVLV HPMASRRQQR RRQARVTCVL I WVVGGLLS ...String:
ASSWPPLELQ SSNQSQLFPQ NATACDNAPE AWDLLHRVLP TFIISICFFG LLGNLFVLLV FLLPRRQLNV AEIYLANLAA SDLVFVLGL PFWAENIWNQ FNWPFGALLC RVINGVIKAN LFIKIFLVVA ICQDRYRVLV HPMASRRQQR RRQARVTCVL I WVVGGLLS IPTFLLRSIQ AVPDLNITAC ILLLPHEAWH FARIVELNIL GFLLPLAAIV FFNYHILASL RTVRLLSGSR EK DRNLRRI TRLVLVVVVA FLVCWAPYHF FAFLEFLFQV QAVRGCFWED FIDLGLQLAN FFAFTNSSLN PVIYVFVGRL FRT KVWELY KQCTPKSLAP ISSS

UniProtKB: B1 bradykinin receptor, Kappa-type opioid receptor, B1 bradykinin receptor

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Macromolecule #2: Nanobody 6

MacromoleculeName: Nanobody 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 18.816033 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAMA QVQLQESGGG LVQAGESLRL SCAASGTIFR LYDMGWYRRV SGNQRELVA SITSGGSTKY GDSVKGRFTI SRDNAKNTVY LQMSSLKPED TAVYYCNAEY RTGIWEELLD GWGQGTQVTV S SHHHHHHE PEA

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Macromolecule #3: R715

MacromoleculeName: R715 / type: protein_or_peptide / ID: 3 / Details: PubChem ID 5311397 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.12635 KDa
SequenceString:
(ACE)KRPPGFS(4J2)I

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7eib

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 232403
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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