7BU7

Structure of human beta1 adrenergic receptor bound to BI-167107 and nanobody 6B9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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This is version 1.1 of the entry. See complete history


Literature

Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR.

Xu, X.Kaindl, J.Clark, M.J.Hubner, H.Hirata, K.Sunahara, R.K.Gmeiner, P.Kobilka, B.K.Liu, X.

(2021) Cell Res 31: 569-579

  • DOI: 10.1038/s41422-020-00424-2
  • Primary Citation of Related Structures:  
    7BTS, 7BU6, 7BU7, 7BVQ

  • PubMed Abstract: 
  • Beta adrenergic receptors (βARs) mediate physiologic responses to the catecholamines epinephrine and norepinephrine released by the sympathetic nervous system. While the hormone epinephrine binds β 1 AR and β 2 AR with similar affinity, the smaller neurotransmitter norepinephrine is approximately tenfold selective for the β 1 AR ...

    Beta adrenergic receptors (βARs) mediate physiologic responses to the catecholamines epinephrine and norepinephrine released by the sympathetic nervous system. While the hormone epinephrine binds β 1 AR and β 2 AR with similar affinity, the smaller neurotransmitter norepinephrine is approximately tenfold selective for the β 1 AR. To understand the structural basis for this physiologically important selectivity, we solved the crystal structures of the human β 1 AR bound to an antagonist carazolol and different agonists including norepinephrine, epinephrine and BI-167107. Structural comparison revealed that the catecholamine-binding pockets are identical between β 1 AR and β 2 AR, but the extracellular vestibules have different shapes and electrostatic properties. Metadynamics simulations and mutagenesis studies revealed that these differences influence the path norepinephrine takes to the orthosteric pocket and contribute to the different association rates and thus different affinities.


    Organizational Affiliation

    School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China. liu_xy@mail.tsinghua.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endolysin,Endolysin,Beta-1 adrenergic receptor chimeraA516Escherichia virus T4Homo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: eT4Tp126ADRB1ADRB1RB1AR
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for D9IEF7 (Enterobacteria phage T4)
Explore D9IEF7 
Go to UniProtKB:  D9IEF7
Find proteins for P08588 (Homo sapiens)
Explore P08588 
Go to UniProtKB:  P08588
PHAROS:  P08588
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
camelid antibody fragmentB128Camelidae mixed libraryMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC, D2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
K [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
P0G (Subject of Investigation/LOI)
Query on P0G

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O [auth A]8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
C21 H26 N2 O4
NWQXBEWHTDRJIP-KRWDZBQOSA-N
 Ligand Interaction
1WV (Subject of Investigation/LOI)
Query on 1WV

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L [auth A](2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate
C17 H32 O4
LVBAGTJIDOCNIJ-INIZCTEOSA-N
 Ligand Interaction
P6G
Query on P6G

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P [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

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N [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

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M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
C, Dalpha-maltoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 377.98α = 90
b = 66.22β = 93.883
c = 47.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references