9lfa

Cryo-EM structure of human bradykinin receptor B1R bound to antagonist ELN441958

Method: ELECTRON MICROSCOPY D_max: 98.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

B1 bradykinin receptor,Kappa-type opioid receptor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 256–279	Mutation：S124K/S132C	Nanobody 6 × 1 A1EJF 7-chloranyl-2-[3-[(9-pyridin-4-yl-3,9-diazaspiro[5.5]undecan-3-yl)carbonyl]phenyl]-3H-isoindol-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9LFA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
22EM Gi bound kappa-opioid receptor in complex with beta01 Deposited 2026-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 54–358（305 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
22ES Gi bound kappa-opioid receptor in complex with difelikefalin Deposited 2026-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 3–380（378 aa）	Not recorded	CLR CHOLESTEROL × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.43 Å
4DJH Structure of the human kappa opioid receptor in complex with JDTic Deposited 2012-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 43–261（219 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain A 263–358（96 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain B 43–261（219 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain B 263–358（96 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358	Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A	JDC (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 2 CIT CITRIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 30% (v/v) PEG400, 400 mM potassium nitrate, lipidic cubic phase, temperature 293K	Resolution 2.90 Å R-free 0.265
4DJH Structure of the human kappa opioid receptor in complex with JDTic Deposited 2012-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 43–261（219 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain A 263–358（96 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain B 43–261（219 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Chain B 263–358（96 aa） Fragment：UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358	Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A Mutation：I135L, C54T, C97A	JDC (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 2 CIT CITRIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 30% (v/v) PEG400, 400 mM potassium nitrate, lipidic cubic phase, temperature 293K	Resolution 2.90 Å R-free 0.265
6B73 Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor Deposited 2017-10-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 54–358（305 aa） Fragment：unp residues 23-128; unp residues 54-358	Mutation：M29W, H124I, L51R, I135L	CVV N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide × 1 CLR CHOLESTEROL × 1 OLA OLEIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM Bis-tris pH 6.5-7.0, 140-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese(II) chloride tetrahydrate, 28-30% PEG400	Resolution 3.10 Å R-free 0.275
6B73 Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor Deposited 2017-10-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 54–358（305 aa） Fragment：unp residues 23-128; unp residues 54-358	Mutation：M29W, H124I, L51R, I135L	CVV N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide × 1 CLR CHOLESTEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM Bis-tris pH 6.5-7.0, 140-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese(II) chloride tetrahydrate, 28-30% PEG400	Resolution 3.10 Å R-free 0.275
6VI4 Nanobody-Enabled Monitoring of Kappa Opioid Receptor States Deposited 2020-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 54–358（305 aa） Chain B 54–358（305 aa）	Mutation：I135L Mutation：I135L	JDC (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 2 CLR CHOLESTEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM Tris pH 7.0, 360-400 mM Ammonium citrate dibasic, 28-32% PEG400	Resolution 3.30 Å R-free 0.271
7T10 CryoEM structure of somatostatin receptor 2 in complex with somatostatin-14 and Gi3 Deposited 2021-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 254–270（17 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7T11 CryoEM structure of somatostatin receptor 2 in complex with Octreotide and Gi3. Deposited 2021-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 254–270（17 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7UL2 CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6 Deposited 2022-04-03	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 246–279（34 aa）	Not recorded	Q6Q 2-[[1-(7-chloranylquinolin-4-yl)-5-(2,6-dimethoxyphenyl)pyrazol-3-yl]carbonylamino]adamantane-2-carboxylic acid × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
7UL5 CryoEM Structure of Inactive SSTR2 bound to Nb6 Deposited 2022-04-03	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 256–271（16 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7Y1F Cryo-EM structure of human k-opioid receptor-Gi complex Deposited 2022-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 54–358（305 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7YIT Molecular mechanism of biased signaling at the kappa opioid receptor Deposited 2022-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 54–358（305 aa）	Mutation：I135L,S324C	IVB nalfurafine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.7；293 K；40-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese (II) chloride tetrahydrate 28-30% PEG400	Resolution 3.30 Å R-free 0.335
8DZP momSalB bound Kappa Opioid Receptor in complex with Gi1 Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 54–358（305 aa） Fragment：UNP residues 54-339	Mutation：I135L	U99 methyl (2S,4aR,6aR,7R,9S,10aS,10bR)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-dimethyl-4,10-dioxododecahydro-2H-naphtho[2,1-c]pyran-7-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.71 Å
8DZQ momSalB bound Kappa Opioid Receptor in complex with GoA Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 54–358（305 aa） Fragment：UNP residues 54-339	Mutation：I135L	U99 methyl (2S,4aR,6aR,7R,9S,10aS,10bR)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-dimethyl-4,10-dioxododecahydro-2H-naphtho[2,1-c]pyran-7-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.82 Å
8DZR GR89,696 bound Kappa Opioid Receptor in complex with gustducin Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 54–338（285 aa） Fragment：UNP residues 54-339	Mutation：I135L	U9I methyl (3R)-4-[(3,4-dichlorophenyl)acetyl]-3-[(pyrrolidin-1-yl)methyl]piperazine-1-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.61 Å
8DZS GR89,696 bound Kappa Opioid Receptor in complex with Gz Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 54–358（305 aa）	Mutation：I135L	U9I methyl (3R)-4-[(3,4-dichlorophenyl)acetyl]-3-[(pyrrolidin-1-yl)methyl]piperazine-1-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.65 Å
8F7W Gi bound kappa-opioid receptor in complex with dynorphin Deposited 2022-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 3–380（378 aa）	Not recorded	CLR CHOLESTEROL × 3 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8FEG CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1 Deposited 2022-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 54–358（305 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.54 Å
8HNN Structure of CXCR3 complexed with antagonist SCH546738 Deposited 2022-12-08	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 252–273（22 aa）	Not recorded	43I 3-azanyl-6-chloranyl-5-[(3S)-4-[1-[(4-chlorophenyl)methyl]piperidin-4-yl]-3-ethyl-piperazin-1-yl]pyrazine-2-carboxamide × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8K2W Structure of CXCR3 complexed with antagonist AMG487 Deposited 2023-07-14	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 252–273（22 aa）	Not recorded	CLR CHOLESTEROL × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 LPC [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE × 1 FI6 N-[(1R)-1-[3-(4-ethoxyphenyl)-4-oxidanylidene-pyrido[2,3-d]pyrimidin-2-yl]ethyl]-N-(pyridin-3-ylmethyl)-2-[4-(trifluoromethyloxy)phenyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8VVE Kappa opioid receptor:Galphai protein in complex with inverse agonist norBNI Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–380（380 aa）	Not recorded	A1AD6 (4bS,8R,8aS,10aS,11R,14aS,19aR,20bR)-7,12-bis(cyclopropylmethyl)-5,6,7,8,9,10,11,12,13,14,20,20b-dodecahydro-19aH-4,8:11,15-dimethanobis[1]benzofuro[2,3-a:3',2'-i]dipyrido[4,3-b:3',4'-h]carbazole-1,8a,10a,18-tetrol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8VVF Kappa opioid receptor:Galphai protein in complex with inverse agonist JDTic Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–380（380 aa）	Not recorded	JDC (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8VVG Kappa opioid receptor in complex with heterotrimerig Gi protein, bound to inverse agonist GB18 Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–380（380 aa）	Not recorded	A1AD5 methyl (2R,3R,3aS,5aR,9aS,9bS)-3-methyl-2-[(2S,6S)-6-methylpiperidin-2-yl]-1,2,3,3a,6,7,8,9,9a,9b-decahydro-3,5a-epoxycyclopenta[a]naphthalene-4-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9D61 Kappa opioid receptor:Galphai protein in complex with inverse agonist JDTic , no scFv16 Deposited 2024-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–380（380 aa）	Not recorded	JDC (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9L60 Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15 Deposited 2024-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 3–380（378 aa）	Not recorded	CLR CHOLESTEROL × 2 A1D6C 9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9LFC Cryo-EM structure of human bradykinin receptor B1R bound to antagonist R715 Deposited 2025-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: dimeric	Chain A 256–279（24 aa）	Mutation：S124K/S132C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9LFD Cryo-EM structure of human bradykinin receptor B2R bound to antagonist Win64338 Deposited 2025-01-08	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 255–284（30 aa）	Mutation：S144K/C146W	A1EJK Win64338 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9UWV SalA bound Kappa Opioid Receptor in complex with Gi Deposited 2025-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 3–380（378 aa）	Not recorded	A1EQK methyl (2~{S},4~{a}~{R},6~{a}~{R},7~{R},9~{S},10~{a}~{S},10~{b}~{R})-9-acetyloxy-2-(furan-3-yl)-6~{a},10~{b}-dimethyl-4,10-bis(oxidanylidene)-2,4~{a},5,6,7,8,9,10~{a}-octahydro-1~{H}-benzo[f]isochromene-7-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9UXU SalA bound Kappa Opioid Receptor in complex with Gi Deposited 2025-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain R 3–380（378 aa） Chain r 3–380（378 aa）	Not recorded	A1EQK methyl (2~{S},4~{a}~{R},6~{a}~{R},7~{R},9~{S},10~{a}~{S},10~{b}~{R})-9-acetyloxy-2-(furan-3-yl)-6~{a},10~{b}-dimethyl-4,10-bis(oxidanylidene)-2,4~{a},5,6,7,8,9,10~{a}-octahydro-1~{H}-benzo[f]isochromene-7-carboxylate × 2 Y01 CHOLESTEROL HEMISUCCINATE × 2 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9UXX SalA bound Kappa Opioid Receptor homodimer Deposited 2025-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain R 3–380（378 aa） Chain r 3–380（378 aa）	Not recorded	A1EQK methyl (2~{S},4~{a}~{R},6~{a}~{R},7~{R},9~{S},10~{a}~{S},10~{b}~{R})-9-acetyloxy-2-(furan-3-yl)-6~{a},10~{b}-dimethyl-4,10-bis(oxidanylidene)-2,4~{a},5,6,7,8,9,10~{a}-octahydro-1~{H}-benzo[f]isochromene-7-carboxylate × 2 CLR CHOLESTEROL × 12 PLM PALMITIC ACID × 2 Y01 CHOLESTEROL HEMISUCCINATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9V6O Cryo-EM structure of human kappa opioid receptor - G protein signaling complex bound with nalfurafine. Deposited 2025-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 54–380（327 aa）	Not recorded	IVB nalfurafine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
9W49 Cryo-EM structure of human kappa opioid receptor -G protein signaling complex bound with U-50488H Deposited 2025-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 54–358（305 aa）	Mutation：I135L	A1LWX 2-(3,4-dichlorophenyl)-~{N}-methyl-~{N}-[(1~{R},2~{R})-2-pyrrolidin-1-ylcyclohexyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

31 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OPRK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 231–254； UniProt 256–279

B1 bradykinin receptor,Kappa-type opioid receptor

Homo sapiens

UniProt P46663

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–231 Chain A； UniProt 256–341	Mutation：S124K/S132C	Nanobody 6 × 1 A1EJF 7-chloranyl-2-[3-[(9-pyridin-4-yl-3,9-diazaspiro[5.5]undecan-3-yl)carbonyl]phenyl]-3H-isoindol-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9LFA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EIB Cryo-EM structure of the type 1 bradykinin receptor in complex with the des-Arg10-kallidin and an Gq protein Deposited 2021-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 2–350（349 aa）	Mutation：F126W	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9LFC Cryo-EM structure of human bradykinin receptor B1R bound to antagonist R715 Deposited 2025-01-08	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: dimeric	Chain A 2–231（230 aa） Chain A 256–341（86 aa）	Mutation：S124K/S132C Mutation：S124K/S132C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BKRB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 2–231 Author chain A； PDBConstruct 255–340； UniProt 256–341

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9lfa
Deposition date deposition_date	2025-01-08
Structure title title	Cryo-EM structure of human bradykinin receptor B1R bound to antagonist ELN441958
Keywords keywords	GPCR, bradykinin receptor, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.57 Å
Radius of gyration Rg (electron density) rg_electron	27.40 Å
Forward intensity I(0) i0	52018500.00
Molecular weight molecular_weight	39615.0 kDa
Excluded volume excluded_volume	39353 Å³
Envelope volume envelope_volume	67347 Å³
Hydration-shell volume shell_volume	22641 Å³
Envelope diameter envelope_diameter	103.8 Å
Shell Rg shell_rg	31.63 Å
Envelope Rg envelope_rg	27.92 Å
Shape Rg shape_rg	27.34 Å
Total Rg total_rg	27.86 Å
Total atoms total_atoms	3032
Residues n_residues	390
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.5 Å
Rg (real space) rg_real	27.99 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	5.2020e+07
I(0) uncertainty (real space) i0_real_error	8.4700e+05
Rg (reciprocal space) rg_reciprocal	27.86 Å
I(0) (reciprocal space) i0_reciprocal	52010000.0000
Solution quality estimate total_estimate	0.7884
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.616
Kurtosis Kurtosis kurtosis	-0.215
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7309000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.591; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.536; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	B1 bradykinin receptor,Kappa-type opioid receptor
Molecular weight formula_weight	38958.9 kDa
Mutation mutation	S124K/S132C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3032

ASSWPPLELQSSNQSQLFPQNATACDNAPEAWDLLHRVLPTFIISICFFGLLGNLFVLLVFLLPRRQLNVAEIYLANLAASDLVFVLGLPFWAENIWNQFNWPFGALLCRVINGVIKANLFIKIFLVVAICQDRYRVLVHPMASRRQQRRRQARVTCVLIWVVGGLLSIPTFLLRSIQAVPDLNITACILLLPHEAWHFARIVELNILGFLLPLAAIVFFNYHILASLRTVRLLSGSREKDRNLRRITRLVLVVVVAFLVCWAPYHFFAFLEFLFQVQAVRGCFWEDFIDLGLQLANFFAFTNSSLNPVIYVFVGRLFRTKVWELYKQCTPKSLAPISSS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Nanobody 6
Molecular weight formula_weight	18816.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAMAQVQLQESGGGLVQAGESLRLSCAASGTIFRLYDMGWYRRVSGNQRELVASITSGGSTKYGDSVKGRFTISRDNAKNTVYLQMSSLKPEDTAVYYCNAEYRTGIWEELLDGWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	7-chloranyl-2-[3-[(9-pyridin-4-yl-3,9-diazaspiro[5.5]undecan-3-yl)carbonyl]phenyl]-3H-isoindol-1-one
Molecular weight formula_weight	501.0 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	198063

fit	/app/data/saxs_computation/lf/9lfa/9lfa.fit
pddf	/app/data/pr_computation/lf/9lfa/9lfa.pr.out
profile	/app/data/saxs_computation/lf/9lfa/9lfa.dat

Cryo-EM structure of human bradykinin receptor B1R bound to antagonist ELN441958

1. Protein Identity and Related Structures Protein Identity & Related Structures

B1 bradykinin receptor,Kappa-type opioid receptor

State in the Current Structure

Other States of the Same Protein in the Database

B1 bradykinin receptor,Kappa-type opioid receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)