Rhodopsin 3D structures

3D structures of rhodopsin

Updated on 28-May-2025

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• Rhodopsin (Rn)
  • 3cap, 5te3, 5te5 – bRn - bovine
    
  • 6ofj – bRn – Cryo EM
    
  • 2j4y, 4bez - bRn (mutant)
    
  • 1vqx, 1nzs – bRn C terminal – NMR
    
  • 1edx - bRn N terminal – NMR
    
  • 1eds, 1edv, 1edw – bRn intradiskal loop – NMR
    
  • 1fdf – bRn helix 7 - NMR
    
  • 3qc9 – bRn + Mg + ADP
    
  • 1f88, 1gzm, 1hzx, 1jfp, 1l9h, 1u19, 2i35, 2i36, 2i37, 2ped, 3c9l, 3oax - bRn + retinal
    
  • 7zbc, 7zbe, 8a6c, 8a6d, 8a6e - bRn + detergents + retinal – cubic phase
    
  • 3cap, 5te3 - bRn
    
  • 2j4y, 4bez - bRn (mutant)
    
  • 1jfp, 1f88, 5te5 - bRn + retinal
    
  • 3c9m, 5dys - bRn (mutant) + retinal
    
  • 3aym, 3ayn, 2z73, 2ziy, 4ww3 – Rn + retinal – Flying squid
    
  • 6i9k – Rn1 + retinal + lipid – spider
    
  • 1xio – AnRn - Anabaena
    
  • 2m3g – AnRn – NMR
    
  • 4tl3 - AnRn (mutant) + retinal
    
  • 4hyj - Rn + retinal + lipid – Exiguobacterium Sibiricum
    
  • 3am6 – AaRn-2 + cholesterol + retinal – Acetabularia acetabulum
    
  • 5awz, 5ax0, 5ax1 – AaRn-1 + retinal
    
  • 4tl3 – AaRn-1 (mutant)
    
  • 6sqg - Rn + retinal + lipid – lake phycodnavirus
    
  • 6kfq - Rn + retinal + lipid – Rubrobacter xylanophilus
    
• Rhodopsin complex with protein
  • 2x72 – bRn + retinal + guanine nucleotide-binding protein peptide
    
  • 3dqb, 4a4m, 4j4q - bRn + guanine nucleotide-binding protein peptide
    
  • 4bey - bRn (mutant) + guanine nucleotide-binding protein peptide
    
  • 6nwe - bRn + peptide + detergents
    
  • 6pel - bRn + peptide + detergents + citronellol
    
  • 6pgs - bRn + peptide + detergents + geraniol
    
  • 6ph7 - bRn + peptide + detergents + nerol
    
  • 5en0 - bRN (mutant) + guanine nucleotide-binding protein peptide + retinal
    
  • 4pxf – bRn + arrestin peptide
    
  • 5wkt – bRn + transducin peptide
    
  • 6fuf – bRn + G0 + retinal
    
  • 8fcz, 8fd1 – bRn + nanobody
    
  • 6oy9 – bRn (mutant) + transducin + GI + retinal – Cryo EM
    
  • 6qno, 6oya – bRn (mutant) + transducin + antibody + GI + retinal – Cryo EM
    
• Sensory rhodopsin II
  • 1gu8, 1gue, 1h68, 1jgj, 3qap, 3qdc – NpSRII – Natronomonas pharaonis
    
  • 2ksy – NpSRII - NMR
    
  • 9h20 - NpSRII + retinal
    
  • 1h2s, 2f93, 2f95, 5jjn, 5jjj, 5jjf, 5jje – NpSRII + Rn II transducer
    
  • 4gyc - NpSRII (mutant) + Rn II transducer
    
• Sodium pump rhodopsin
  • 4xtl, 4xtn, 4xto, 3x3b, 3x3c, 5jrf – DeRn – Dokdonia eikastra
    
  • 5jrf – DeRn + detergent + I
    
  • 6yc3, 6rex, 6rez, 6rf0, 6rf1, 6rf4, 6rf5, 6rf6, 6rf7, 6tk1, 6tk2, 6tk3, 6tk4, 6tk5, 6tk6, 6tk7, 6xyt, 6yby, 6ybz, 6yc0, 6yc1, 6yc2, 6yc4, 7q36 – DeRn + detergent + Na + retinal
    
  • 6rf3, 6rf9, 6rfa, 6rfb, 6rfc, 6yt4 – DeRn (mutant) + detergent + Na + retinal
    
• Chloride pump rhodopsin
  • 5g28, 5g2a, 5b2n, 5fjg, 5g54, 5ztk, 5ztl, 6ab9, 6aba, 6jy6, 6jy7, 6jy8, 6jy9, 6jya, 6jyb, 6jyc, 6jyd, 6jye, 6jyf, 7cri, 7crj, 7crk, 7crl, 7crs, 7crt, 7crx, 7cry, 7vgt, 7vgu, 7vgv – NmRn + retinal – Nonlabens marinus
    
  • 7o8f, 7o8g, 7o8h, 7o8i, 7o8j, 7o8k, 7o8l, 7o8m, 7o8n, 7o8o, 7o8p, 7o8r, 7o8q, 7o8s, 7o8t, 7o8u, 7o8v, 7o8y, 7o8z – NmRn + retinal – serial millisecond crystallography
    
  • 5g2c, 5g2d - NmRn (mutant) + retinal
    
  • 6wp8, 6xl3 – Rn (mutant) + detergent + retinal – Mastigocladopsis repens
    
• Metarhodopsin II
  • 3pqr – bMRn + guanine nucleotide-binding protein peptide + retinal
    
  • 3pxo - bMRn + retinal
    
  • 1ln6 - bMRn + retinal
    
• Bathorhodopsin
  • 2g87 - bBRn + retinal
    
• Lumirhodopsin
  • 2hpy - bLRn + retinal
    
• Halorhodopsin see Bacteriorhodopsin
• Archaerhodopsin see Bacteriorhodopsin
• Proteorhodopsin see Bacteriorhodopsin
• Xanthorhodopsin see Bacteriorhodopsin
• Bestrhodopsin (Rn-Rn-bestrophin)
  • 7pl9 - Rn + retinal – Phaeocystis – Cryo EM
    
• Deltarhodopsin see Bacteriorhodopsin
• Cyanorhodopsin
  • 6lm0 - CRn + detergents + retinal – Cyanobacteria calothrix
    
  • 6lm1 - CRn + detergents + retinal – Cyanobacteria tolypothrix
    
• Viral rhodopsin
  • 6sqg, 7akw, 7akx, 7aky - Rn + detergents – organic lake phycodnavirus
    

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Michal Harel, Jaime Prilusky, Joel L. Sussman