1iw9
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1iw9 |SIZE=350|CAPTION= <scene name='initialview01'>1iw9</scene>, resolution 2.5Å | |PDB= 1iw9 |SIZE=350|CAPTION= <scene name='initialview01'>1iw9</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1dze|1dze]], [[1iw6|1IW6]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iw9 OCA], [http://www.ebi.ac.uk/pdbsum/1iw9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iw9 RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] | ||
[[Category: Takeda, K.]] | [[Category: Takeda, K.]] | ||
| - | [[Category: L2P]] | ||
| - | [[Category: L3P]] | ||
| - | [[Category: RET]] | ||
[[Category: 7 transmembrane helice]] | [[Category: 7 transmembrane helice]] | ||
[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
| Line 37: | Line 37: | ||
[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:25:30 2008'' |
Revision as of 18:25, 30 March 2008
| |||||||
| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Related: | 1dze, 1IW6
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of the M Intermediate of Bacteriorhodopsin
Overview
Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.
About this Structure
1IW9 is a Single protein structure of sequence from Halobacterium salinarum. Full crystallographic information is available from OCA.
Reference
Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix., Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T, J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615
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