4O9R

Human Smoothened Receptor structure in complex with cyclopamine

• PDB DOI: https://doi.org/10.2210/pdb4O9R/pdb

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


• Deposited: 2014-01-02 Released: 2014-03-05 
• Deposition Author(s): Wang, C., Weierstall, U., James, D., White, T.A., Wang, D., Liu, W., Spence, J.C.H., Doak, R.B., Nelson, G., Fromme, P., Fromme, R., Grotjohann, I., Kupitz, C., Zatsepin, N.A., Liu, H., Basu, S., Wacker, D., Han, G.W., Katritch, V., Boutet, S., Messerschmidt, M., Willams, G.J., Koglin, J.E., Seibert, M.M., Klinker, M., Gati, C., Shoeman, R.L., Barty, A., Chapman, H.N., Kirian, R.A., Beyerlein, K.R., Stevens, R.C., Li, D., Shah, S.T.A., Howe, N., Caffrey, M., Cherezov, V., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.278 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

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

(2014) Nat Commun 5: 3309-3309

• PubMed: 24525480 
• DOI: https://doi.org/10.1038/ncomms4309
• Primary Citation of Related Structures:  
  4O9R


• PubMed Abstract: 
  

  Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.

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Organizational Affiliation: 

Department of Physics, Arizona State University, Tempe, Arizona 85287, 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: 52.81 kDa 
• Atom Count: 3,419 
• Modelled Residue Count: 441 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Smoothened homolog/Soluble cytochrome b562 chimeric protein	A	468	Homo sapiens, Escherichia coli	Mutation(s): 3  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q99835 (Homo sapiens) Explore Q99835  Go to UniProtKB:  Q99835
PHAROS:  Q99835 GTEx:  ENSG00000128602
UniProt Groups	P0ABE7Q99835

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CY8	B [auth A]	Cyclopamine C27 H41 N O2 QASFUMOKHFSJGL-LAFRSMQTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CY8	BindingDB:  4O9R	Ki: 12.7 (nM) from 1 assay(s)
		Kd: 12.4 (nM) from 1 assay(s)
		IC50: min: 64, max: 1900 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.278 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.11577/1255979

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.5	α = 90
b = 157.3	β = 97
c = 52.4	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: 2014-03-05 
Deposition Author(s): Wang, C., Weierstall, U., James, D., White, T.A., Wang, D., Liu, W., Spence, J.C.H., Doak, R.B., Nelson, G., Fromme, P., Fromme, R., Grotjohann, I., Kupitz, C., Zatsepin, N.A., Liu, H., Basu, S., Wacker, D., Han, G.W., Katritch, V., Boutet, S., Messerschmidt, M., Willams, G.J., Koglin, J.E., Seibert, M.M., Klinker, M., Gati, C., Shoeman, R.L., Barty, A., Chapman, H.N., Kirian, R.A., Beyerlein, K.R., Stevens, R.C., Li, D., Shah, S.T.A., Howe, N., Caffrey, M., Cherezov, V., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2018-02-14
  Changes: Data collection
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Refinement description