4NC3

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

• PDB DOI:  https://doi.org/10.2210/pdb4NC3/pdb

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


• 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: 2.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

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: 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 53.26 kDa 
• Atom Count: 3,123 
• Modelled Residue Count: 370 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of human 5-hydroxytryptamine receptor 2B and E. Coli soluble cytochrome b562	A	430	Homo sapiens, Escherichia coli	Mutation(s): 4  Gene Names: HTR2B, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41595 (Homo sapiens) Explore P41595  Go to UniProtKB:  P41595
PHAROS:  P41595
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	P0ABE7P41595

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGA	N [auth A], O [auth A]	DIACYL GLYCEROL C39 H76 O5 UHUSDOQQWJGJQS-QNGWXLTQSA-N
ERM	C [auth A]	Ergotamine C33 H35 N5 O5 XCGSFFUVFURLIX-VFGNJEKYSA-N
CLR	D [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	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	K [auth A], L [auth A], M [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRS	J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.11577/1169541

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.5	α = 90
b = 122.2	β = 90
c = 168.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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