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- EMDB-64536: Cryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64536
TitleCryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with icatibant
Map data
Sample
  • Complex: Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab antibody
    • Complex: B2R-BRIL
      • Protein or peptide: B2 bradykinin receptor,Soluble cytochrome b562
    • Complex: anti-BRIL SRP2070 Fab antibody
      • Protein or peptide: Heavy chain of anti-BRIL SRP2070 fab antibody
      • Protein or peptide: Light chain of anti-BRIL SRP2070 fab antibody
    • Complex: Icatibant
      • Protein or peptide: icatibant
KeywordsGPCR / B2R / bradykinin / icatibant / MEMBRANE PROTEIN
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 / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / vasoconstriction / type 1 angiotensin receptor binding / regulation of vascular permeability / blood circulation / arachidonate secretion / smooth muscle contraction ...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 / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / vasoconstriction / type 1 angiotensin receptor binding / regulation of vascular permeability / blood circulation / arachidonate secretion / smooth muscle contraction / regulation of vasoconstriction / response to salt stress / cell surface receptor protein tyrosine kinase signaling pathway / Peptide ligand-binding receptors / electron transport chain / vasodilation / positive regulation of cytosolic calcium ion concentration / protease binding / G alpha (i) signalling events / G alpha (q) signalling events / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / endosome / iron ion binding / G protein-coupled receptor signaling pathway / inflammatory response / protein heterodimerization activity / heme binding / plasma membrane
Similarity search - Function
Bradykinin receptor B2 / Bradykinin receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / B2 bradykinin receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / Resolution: 3.29 Å
AuthorsKojima A / Kawakami K / Kobayashi K / Matsui TE / Gu Y / Fukuda M / Kato HE
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX222F Japan
Japan Science and TechnologyJPMJPR24OF Japan
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
Japan Society for the Promotion of Science (JSPS)24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25H01338 Japan
Japan Society for the Promotion of Science (JSPS)24KJ0981 Japan
CitationJournal: Biorxiv / Year: 2026
Title: A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design
Authors: Kojima A / Kawakami K / Kobayashi N / Kobayashi K / Matsui TE / Uemoto K / Gu Y / Fukuda M / Kato HE
History
DepositionMay 11, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64536.png

Downloads & links

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Map

FileDownload / File: emd_64536.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 234 pix.
= 194.22 Å		0.83 Å/pix.
x 234 pix.
= 194.22 Å		0.83 Å/pix.
x 234 pix.
= 194.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.24307439 - 0.6066236
Average (Standard dev.)-0.0012283049 (±0.018370612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 194.22 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64536_msk_1.map
Projections & Slices
AxesZYX

Projections

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Histogram (log scale)

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Additional map: #1

Fileemd_64536_additional_1.map
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Half map: #2

Fileemd_64536_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64536_half_map_2.map
Projections & Slices
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Sample components

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Entire : Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab an...

EntireName: Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab antibody
Components
  • Complex: Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab antibody
    • Complex: B2R-BRIL
      • Protein or peptide: B2 bradykinin receptor,Soluble cytochrome b562
    • Complex: anti-BRIL SRP2070 Fab antibody
      • Protein or peptide: Heavy chain of anti-BRIL SRP2070 fab antibody
      • Protein or peptide: Light chain of anti-BRIL SRP2070 fab antibody
    • Complex: Icatibant
      • Protein or peptide: icatibant

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Supramolecule #1: Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab an...

SupramoleculeName: Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: B2R-BRIL

SupramoleculeName: B2R-BRIL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: anti-BRIL SRP2070 Fab antibody

SupramoleculeName: anti-BRIL SRP2070 Fab antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Icatibant

SupramoleculeName: Icatibant / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4

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Macromolecule #1: Heavy chain of anti-BRIL SRP2070 fab antibody

MacromoleculeName: Heavy chain of anti-BRIL SRP2070 fab antibody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.421154 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MEAPAQLLFL LLLWLPSSRA MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKA TLIVDTSSST AFMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS G SSVTLGCL ...String:
MEAPAQLLFL LLLWLPSSRA MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKA TLIVDTSSST AFMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS G SSVTLGCL VKGYFPEPVT LTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PR GCLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

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Macromolecule #2: Light chain of anti-BRIL SRP2070 fab antibody

MacromoleculeName: Light chain of anti-BRIL SRP2070 fab antibody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.065002 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MEAPAQLLFL LLLWLPSSRA MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSG TDFTLSINSV ETEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN F YPKDINVK ...String:
MEAPAQLLFL LLLWLPSSRA MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSG TDFTLSINSV ETEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN F YPKDINVK WKIDGSERQN GVLNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

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Macromolecule #3: B2 bradykinin receptor,Soluble cytochrome b562

MacromoleculeName: B2 bradykinin receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.839855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPLSVREDSV PTTASFSADM LNVTLQGPTL NGTFAQSKCP QVEWLGWLNT IQPPFLWVLF VLATLENIFV LSVFCLHKSS CTVAEIYLG NLAAADLILA CGLPFWAITI SNNFDWLFGE TLCRVVNAII SMNLYSSICF LMLVSIDRYL ALVKTMSMGR M RGVRWAKL ...String:
GPLSVREDSV PTTASFSADM LNVTLQGPTL NGTFAQSKCP QVEWLGWLNT IQPPFLWVLF VLATLENIFV LSVFCLHKSS CTVAEIYLG NLAAADLILA CGLPFWAITI SNNFDWLFGE TLCRVVNAII SMNLYSSICF LMLVSIDRYL ALVKTMSMGR M RGVRWAKL YSLVIWGCTL LLSSPMLVFR TMKEYSDEGH NVTACVISYP SLIWEVFTNM LLNVVGFLLP LSVITFCTMQ IM QVLADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALK LANEGK VKEAQAAAEQ LKTTRNAYIQ KYLKEIQTER RATVLVLVVL LLFIICWLPF QISTFLDTLH RLGILSSCQD ERII DVITQ IASFMAYSNS CLNPLVYVIV GKRFRKKSWE VYQGVCQKGG CRSEPIQMEN SMGTLRTSIS VERQIHKLQD WAGSR QLEV LFQ

UniProtKB: B2 bradykinin receptor, Soluble cytochrome b562, B2 bradykinin receptor

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Macromolecule #4: icatibant

MacromoleculeName: icatibant / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.307548 KDa
SequenceString:
(DAR)RP(HYP)G(TIH)S(A1EJL)(OIC)R

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187522
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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