9UVT | pdb_00009uvt

Cryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with icatibant

• PDB DOI: https://doi.org/10.2210/pdb9UVT/pdb
• EM Map EMD-64536: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus, Homo sapiens, Escherichia coli, synthetic construct
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-05-11 Released: 2026-05-06 
• Deposition Author(s): Kojima, A., Kawakami, K., Kobayashi, K., Matsui, T.E., Gu, Y., Fukuda, M., Kato, H.E.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design

Kojima, A., Kawakami, K., Kobayashi, N., Kobayashi, K., Matsui, T.E., Uemoto, K., Gu, Y., Fukuda, M., Kato, H.E.

(2026) bioRxiv 

• DOI: https://doi.org/10.64898/2026.04.02.716066

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 113.63 kDa 
• Atom Count: 4,529 
• Modeled Residue Count: 573 
• Deposited Residue Count: 1,022 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of anti-BRIL SRP2070 fab antibody	A [auth H]	290	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of anti-BRIL SRP2070 fab antibody	B [auth L]	235	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B2 bradykinin receptor,Soluble cytochrome b562	C [auth A]	487	Homo sapiens, Escherichia coli	Mutation(s): 3  Gene Names: BDKRB2, BKR2, cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P30411 (Homo sapiens) Explore P30411  Go to UniProtKB:  P30411
PHAROS:  P30411 GTEx:  ENSG00000168398
UniProt Groups	P30411P0ABE7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
icatibant	D [auth B]	10	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EJL	D [auth B]	D-PEPTIDE LINKING	C10 H11 N O2		--
DAR	D [auth B]	D-PEPTIDE LINKING	C6 H15 N4 O2		--
HYP	D [auth B]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
OIC	D [auth B]	L-PEPTIDE LINKING	C9 H15 N O2		--
TIH	D [auth B]	L-PEPTIDE LINKING	C7 H9 N O2 S		ALA

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Kojima, A., Kawakami, K., Kobayashi, K., Matsui, T.E., Gu, Y., Fukuda, M., Kato, H.E.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX222F
Japan Science and Technology	Japan	JPMJPR24OF
Japan Society for the Promotion of Science (JSPS)	Japan	25K09525
Japan Society for the Promotion of Science (JSPS)	Japan	24H02262
Japan Society for the Promotion of Science (JSPS)	Japan	25H01338
Japan Society for the Promotion of Science (JSPS)	Japan	24KJ0981

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release