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PDBsum entry 3cap
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Signaling protein PDB id
3cap

 

 

 

 

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Contents
Protein chains
326 a.a. *
Ligands
NAG-NAG-BMA-BMA ×2
NAG-NAG ×2
BGL ×6
PLM ×2
Waters ×10
* Residue conservation analysis
PDB id:
3cap
Name: Signaling protein
Title: Crystal structure of native opsin: the g protein-coupled receptor rhodopsin in its ligand-free state
Structure: Rhodopsin. Chain: a, b. Other_details: this protein is ligand-free rhodopsin, opsin.
Source: Bos taurus. Bovine. Organism_taxid: 9913
Resolution:
2.90Å     R-factor:   0.231     R-free:   0.266
Authors: J.H.Park,P.Scheerer,K.P.Hofmann,H.-W.Choe,O.P.Ernst
Key ref: J.H.Park et al. (2008). Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature, 454, 183-187. PubMed id: 18563085
Date:
20-Feb-08     Release date:   24-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02699  (OPSD_BOVIN) -  Rhodopsin from Bos taurus
Seq:
Struc: 		348 a.a.
326 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Nature 454:183-187 (2008)
PubMed id: 18563085  
 
 
Crystal structure of the ligand-free G-protein-coupled receptor opsin.
J.H.Park, P.Scheerer, K.P.Hofmann, H.W.Choe, O.P.Ernst.
 
  ABSTRACT  
 
In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 ångström (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3qak
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PDB codes: 2ydo 2ydv
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PDB codes: 3pqr 3pxo
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PDB code: 3p0g
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PDB code: 3kj6
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PDB code: 2k9p
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PDB code: 3dqb
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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