Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53259.86 
• Atom Count: 3116 
• Residue Count: 430 
• Unique protein chains: 1

4NC3

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

• DOI: 10.2210/pdb4NC3/pdb

• Classification: SIGNALING PROTEIN ELECTRON TRANSPORT
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 4 


• Deposited: 2013-10-23 Released: 2013-12-18 
• Deposition Author(s): 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.A., 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.H., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 

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

• PubMed: 24357322 
• DOI: 10.1126/science.1244142


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562	A	430	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: cybC, HTR2B
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  5-HT2B serotonin receptor with bound ergotamine
Find proteins for P0ABE7 (Escherichia coli) Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens) Go to Gene View: HTR2B Go to UniProtKB:  P41595

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	A	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
DGA	A	DIACYL GLYCEROL C39 H76 O5 UHUSDOQQWJGJQS-QNGWXLTQSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ERM	A	Ergotamine C33 H35 N5 O5 XCGSFFUVFURLIX-VFGNJEKYSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRIS BUFFER C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CLR	A	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 61.500	α = 90.00
b = 122.200	β = 90.00
c = 168.500	γ = 90.00

Software Package:

Software Name	Purpose
CrystFEL	data reduction
PHASER	phasing
PHENIX	refinement
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-23 
• Released Date: 2013-12-18 
• Deposition Author(s): 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.A., 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.H., Stevens, R.C., Cherezov, V., GPCR Network (GPCR)

Revision History 

• Version 1.0: 2013-12-18
  Type: Initial release
• Version 1.1: 2014-01-22
  Type: Database references
• Version 1.2: 2017-06-07
  Type: Database references, Structure summary
• Version 1.3: 2018-02-14
  Type: Data collection