4O9R | pdb_00004o9r

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 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Models: experimental

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 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.
The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, California 92037, USA.
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany.
Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.
SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
1] SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA [2] Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden.
1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany [2] Departamento de Química, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid 28049, Spain.
Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, Heidelberg 69120, Germany.
1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany [2] Department of Physics, University of Hamburg, Hamburg 22761, Germany [3] Center for Ultrafast Imaging, Hamburg 22607, Germany.
1] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA [2] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany.
School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.

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 
• Modeled 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 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1255979

Space Group: P 1 2₁ 1

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
• Version 1.5: 2024-10-16
  Changes: Structure summary