4IB4 | pdb_00004ib4

Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4IB4

Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Structural features for functional selectivity at serotonin receptors.

Wacker, D.Wang, C.Katritch, V.Han, G.W.Huang, X.P.Vardy, E.McCorvy, J.D.Jiang, Y.Chu, M.Siu, F.Y.Liu, W.Xu, H.E.Cherezov, V.Roth, B.L.Stevens, R.C.

(2013) Science 340: 615-619

  • DOI: https://doi.org/10.1126/science.1232808
  • Primary Citation Related Structures: 
    4IB4

  • PubMed Abstract: 

    Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or noncanonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. We report biochemical studies showing that the hallucinogen lysergic acid diethylamide, its precursor ergotamine (ERG), and related ergolines display strong functional selectivity for β-arrestin signaling at the 5-HT2B 5-hydroxytryptamine (5-HT) receptor, whereas they are relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, we determined the crystal structure of the human 5-HT2B receptor bound to ERG and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure and function to date, insight into different GPCR signaling pathways is important to better understand both adverse and favorable therapeutic activities.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 51.71 kDa 
  • Atom Count: 3,064 
  • Modeled Residue Count: 375 
  • Deposited Residue Count: 430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562430Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR2BcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens)
Explore P41595 
Go to UniProtKB:  P41595
PHAROS:  P41595
GTEx:  ENSG00000135914 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41595
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ERM

Query on ERM



Download:Ideal Coordinates CCD File
B [auth A]Ergotamine
C33 H35 N5 O5
XCGSFFUVFURLIX-VFGNJEKYSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
D [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLB

Query on OLB



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
E [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
C [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.571α = 90
b = 119.75β = 90
c = 170.607γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
BUSTERrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 1.2: 2013-04-10
    Changes: Database references
  • Version 1.3: 2013-05-15
    Changes: Database references
  • Version 1.4: 2017-06-07
    Changes: Database references, Structure summary
  • Version 1.5: 2017-11-15
    Changes: Refinement description
  • Version 1.6: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.7: 2024-11-06
    Changes: Structure summary