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- PDB-9uvu: Cryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL ... -

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Basic information

Entry
Database: PDB / ID: 9uvu
TitleCryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with icatibant, focused on receptor
Components
  • B2 bradykinin receptor,Soluble cytochrome b562
  • icatibant
KeywordsMEMBRANE PROTEIN / GPCR / B2R / bradykinin / icatibant
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)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.69 Å
AuthorsKojima, A. / Kawakami, K. / Kobayashi, K. / Matsui, T.E. / Gu, Y. / Fukuda, M. / Kato, H.E.
Funding support Japan, 6items
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)JP24KJ0981 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, T.E. / Uemoto, K. / Gu, Y. / Fukuda, M. / Kato, H.E.
History
DepositionMay 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 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

Downloads & links

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Assembly

Deposited unit
B: icatibant
A: B2 bradykinin receptor,Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)56,1472
Polymers56,1472
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/peptide icatibant


Mass: 1307.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein B2 bradykinin receptor,Soluble cytochrome b562 / B2R / BK-2 receptor / Cytochrome b-562


Mass: 54839.855 Da / Num. of mol.: 1 / Mutation: M258W/H353I/R357L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: BDKRB2, BKR2, cybC / Production host: Homo sapiens (human) / References: UniProt: P30411, UniProt: P0ABE7
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

Component
IDNameTypeEntity IDParent-IDSource
1Icatibant-bound B2R-BRIL in complex with anti-BRIL SRP2070 Fab antibody, focused on receptorCOMPLEX#2, #10MULTIPLE SOURCES
2B2R-BRILCOMPLEX#21RECOMBINANT
3IcatibantCOMPLEX#11SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
22Escherichia coli (E. coli)562
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3

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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: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187522 / Symmetry type: POINT
RefinementResolution: 3.69→3.69 Å / Cor.coef. Fo:Fc: 0.782 / WRfactor Rwork: 0.445 / SU B: 33.217 / SU ML: 0.493 / Average fsc free: 0 / Average fsc overall: 0.7756 / Average fsc work: 0.7756 / ESU R: 0.929
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4451 15778 -
all0.445 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 117.294 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0122263
ELECTRON MICROSCOPYr_bond_other_d00.0162232
ELECTRON MICROSCOPYr_angle_refined_deg1.5811.7933090
ELECTRON MICROSCOPYr_angle_other_deg0.8251.7015104
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.6975266
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.5272.72711
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.27510376
ELECTRON MICROSCOPYr_dihedral_angle_6_deg10.4181087
ELECTRON MICROSCOPYr_chiral_restr0.2370.2379
ELECTRON MICROSCOPYr_chiral_restr_other0.5120.21
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.022554
ELECTRON MICROSCOPYr_gen_planes_other0.0060.02531
ELECTRON MICROSCOPYr_nbd_refined0.2210.2605
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1530.22193
ELECTRON MICROSCOPYr_nbtor_refined0.1770.21139
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0630.21214
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1030.259
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0440.21
ELECTRON MICROSCOPYr_mcbond_it9.75110.6551090
ELECTRON MICROSCOPYr_mcbond_other9.74510.6541090
ELECTRON MICROSCOPYr_mcangle_it16.29219.1661352
ELECTRON MICROSCOPYr_mcangle_other16.28919.171353
ELECTRON MICROSCOPYr_scbond_it11.03512.5411173
ELECTRON MICROSCOPYr_scbond_other11.03112.5441174
ELECTRON MICROSCOPYr_scangle_it19.52822.4721738
ELECTRON MICROSCOPYr_scangle_other19.52222.4731739
ELECTRON MICROSCOPYr_lrange_it31.413129.1459349
ELECTRON MICROSCOPYr_lrange_other31.412129.1459350
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.7-3.7961.89311591.89311590.5521.893
3.796-3.90.86311270.86311270.6610.863
3.9-4.0130.63811260.63811260.6880.638
4.013-4.1370.45710550.45710550.7710.457
4.137-4.2720.37310350.37310350.7970.373
4.272-4.4220.33810010.33810010.840.338
4.422-4.5880.34510310.34510310.8530.345
4.588-4.7750.349100.349100.8770.34
4.775-4.9870.388910.388910.8770.38
4.987-5.230.3898470.3898470.8680.389
5.23-5.5120.4088090.4088090.8290.408
5.512-5.8450.4157860.4157860.7740.415
5.845-6.2470.4197240.4197240.7350.419
6.247-6.7460.4416790.4416790.7110.441
6.746-7.3860.4496270.4496270.7110.449
7.386-8.2520.435430.435430.7610.43
8.252-9.5190.3835020.3835020.8340.383
9.519-11.6320.3214160.3214160.8880.321
11.632-16.3430.3323260.3323260.8860.332
16.343-101.260.9161840.9161840.9530.916

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