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- EMDB-63045: Cryo-EM structure of human bradykinin receptor B2R bound to antag... -

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Basic information

Entry
Database: EMDB / ID: EMD-63045
TitleCryo-EM structure of human bradykinin receptor B2R bound to antagonist Win64338
Map data
Sample
  • Complex: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in complex with Nb6, Win64338
    • Protein or peptide: B2 bradykinin receptor,Kappa-type opioid receptor
    • Protein or peptide: Nanobody 6
  • Ligand: Win64338
KeywordsGPCR / bradykinin receptor / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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)
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 B2R bound to antagonist Win64338
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_63045.png

Downloads & links

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Map

FileDownload / File: emd_63045.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.)
0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å		0.89 Å/pix.
x 256 pix.
= 227.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2048432 - 1.8033743
Average (Standard dev.)-0.000465673 (±0.029288549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 227.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63045_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_63045_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 B2R with kappa-type opioid receptor ICL3 in c...

EntireName: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in complex with Nb6, Win64338
Components
  • Complex: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in complex with Nb6, Win64338
    • Protein or peptide: B2 bradykinin receptor,Kappa-type opioid receptor
    • Protein or peptide: Nanobody 6
  • Ligand: Win64338

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Supramolecule #1: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in c...

SupramoleculeName: bradykinin receptor B2R with kappa-type opioid receptor ICL3 in complex with Nb6, Win64338
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56 KDa

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Macromolecule #1: B2 bradykinin receptor,Kappa-type opioid receptor

MacromoleculeName: B2 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: 41.577094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LNVTLQGPTL NGTFAQSKCP QVEWLGWLNT IQPPFLWVLF VLATLENIFV LSVFCLHKSS CTVAEIYLGN LAAADLILAC GLPFWAITI SNNFDWLFGE TLCRVVNAII SMNLYSKIWF LMLVSIDRYL ALVKTMSMGR MRGVRWAKLY SLVIWGCTLL L SSPMLVFR ...String:
LNVTLQGPTL NGTFAQSKCP QVEWLGWLNT IQPPFLWVLF VLATLENIFV LSVFCLHKSS CTVAEIYLGN LAAADLILAC GLPFWAITI SNNFDWLFGE TLCRVVNAII SMNLYSKIWF LMLVSIDRYL ALVKTMSMGR MRGVRWAKLY SLVIWGCTLL L SSPMLVFR TMKEYSDEGH NVTACVISYP SLIWEVFTNM LLNVVGFLLP LSVITFCTMQ IMQVLRSVRL LSGSREKDRN LR RITRLVL VVVAVFVICW LPFQISTFLD TLHRLGILSS CQDERIIDVI TQIASFMAYS NSCLNPLVYV IVGKRFRKKS WEV YQGVCQ KGGCRSEPIQ MENSMGTLRT SISVERQIHK LQDWAGSRQ

UniProtKB: B2 bradykinin receptor, Kappa-type opioid receptor, B2 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: 14.730255 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAQVQLQESG GGLVQAGESL RLSCAASGTI FRLYDMGWYR RVSGNQRELV ASITSGGSTK YGDSVKGRFT ISRDNAKNTV YLQMSSLKP EDTAVYYCNA EYRTGIWEEL LDGWGQGTQV TVSSHHHHHH EPEA

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Macromolecule #3: Win64338

MacromoleculeName: Win64338 / type: ligand / ID: 3 / Number of copies: 1 / Formula: A1EJK
Molecular weightTheoretical: 712.021 Da

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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: GATAN K3 (6k 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: 1.7 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:

7f6h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 252676
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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