4NC3

Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography in lipidic cubic phase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Serial femtosecond crystallography of G protein-coupled receptors.

Liu, W.Wacker, D.Gati, C.Han, G.W.James, D.Wang, D.Nelson, G.Weierstall, U.Katritch, V.Barty, A.Zatsepin, N.A.Li, D.Messerschmidt, M.Boutet, S.Williams, G.J.Koglin, J.E.Seibert, M.M.Wang, C.Shah, S.T.Basu, S.Fromme, R.Kupitz, C.Rendek, K.N.Grotjohann, I.Fromme, P.Kirian, R.A.Beyerlein, K.R.White, T.A.Chapman, H.N.Caffrey, M.Spence, J.C.Stevens, R.C.Cherezov, V.

(2013) Science 342: 1521-1524

  • DOI: https://doi.org/10.1126/science.1244142
  • Primary Citation of Related Structures:  
    4NC3

  • PubMed Abstract: 

    X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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 P41595 (Homo sapiens)
Explore P41595 
Go to UniProtKB:  P41595
PHAROS:  P41595
GTEx:  ENSG00000135914 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41595
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGA
Query on DGA

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
ERM
Query on ERM

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C [auth A]Ergotamine
C33 H35 N5 O5
XCGSFFUVFURLIX-VFGNJEKYSA-N
CLR
Query on CLR

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D [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC
Query on OLC

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E [auth A],
F [auth A],
H [auth A],
I [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA
Query on OLA

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K [auth A],
L [auth A],
M [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM
Query on PLM

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B [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRS
Query on TRS

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J [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

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G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.5α = 90
b = 122.2β = 90
c = 168.5γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references, Structure summary
  • Version 1.3: 2018-02-14
    Changes: Data collection
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary