Myoglobin

From Proteopedia

Revision as of 08:51, 5 November 2019

spinqualitylabelsall models Structure of Sperm whale myoglobin containing protoporphyrin with O2 and sulfate (PDB entry 1a6m) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Contents 1 Function 2 Structural highlights 3 Additional details 4 3D Structures of Myoglobin Function Myoglobin is a globular protein whose function is to store molecular oxygen in muscles (myo = muscles)[1]. It has two main components: a single polypeptide chain, and heme ligand. The heme ligand is only to the surface; the majority of it is buried inside the protein. The overall of myoglobin is approximately disc-shaped with a diameter that is about twice its thickness. The overall fold of the protein is conserved, especially the core of the protein (shown in purple), but the sequence is more on the surface. Metmyoglobin (MMb) is the oxidized form of myoglobin. Structural highlights The globin consists mostly of alpha helices shown in ; it has no beta sheets and its non-helical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The eight structurally conserved alpha helices are labelled . The protein is colored as a N-->C rainbow in this view; the N terminus is blue, while the C terminus is red. The , and specifically the iron atom in the middle of the heme, is what binds oxygen in myoglobin. In this representation, the heme alone is shown in ball and stick form with its C, N and O atoms displayed as grey, blue, and red balls respectively. The iron atom is shown in orange, and is in spacefilling mode to better illustrate its interactions with the heme. The iron is bound by four nitrogen atoms found in the heme ring, as well as an from the protein chain. Which amino acid from the myoglobin protein binds to the iron? Notice that in the oxygenated state, the iron is in the plane of the heme ring. In the (no oxygen) state, the Fe atom is slightly above the plane of the heme, and a second coordinates with the iron in the heme ring. Additional details Oxymyoglobin for myoglobin complex with O2 Porphyrin for porphyrin. Molecular Playground/Myoglobin Myoglobin of Physeter catodon: structure Extremophile Extremophiles Myoglobin-Physeter-catodon-structure (Spanish) Myoglobin (Hebrew) Myoglobin (arabic). 3D Structures of Myoglobin Myoglobin 3D structures

3D Structures of Myoglobin

Updated on 05-November-2019 {{#tree:id=OrganizedByTopic|openlevels=0|

• Mb wild type

• • 2zsn, 2zso, 2zsp, 2zsq, 2zsr, 2zss, 2zst, 2zsx, 2zsy, 2zsz, 2zt0, 2zt1, 2zt2, 2zt3, 2zt4, 3e4n, 3e55, 3e5i, 3e5o, 3ecl, 3ecx, 3ecz, 3ed9, 3eda, 3edb, 2z6s, 1u7r, 1u7s, 1jp6, 1jp8, 1jp9, 1jpb, 1jw8, 1f6h, 1bz6, 1bzp, 1a6k, 1a6n, 1vxa, 1vxb, 1vxc, 1vxd, 1vxe, 1vxf, 1vxg, 1vxh, 1mlq, 1moa, 1mob, 1moc, 1mod, 4mbn, 5mbn, 1mbn, 4nxa, 4pnj, 5iks, 5jom, 5m3s, 5o41, 5oj9, 5oja, 5ojb, 5ojc, 5xl0, 5yce– SwMb - Sperm whale
    
  • 1l2k, 1cq2, 1mbd – SwMb – Neutron
    
  • 1wla, 1hsy, 2v1e, 2v1f, 2v1g, 2v1h, 2v1i, 2v1j, 2v1k, 4dc7, 4dc8, 5cn4, 5cn5, 5cn6, 5cn7, 5cn8, 5cn9, 5cnb, 5cnc, 5cnd, 5cne, 5cnf, 5cng, 5d5r, 5zze – hoMb - horse
    
  • 1m6m, 1mwd, 1mnh, 1mnj, 1mnk, 1ycb, 1pmb – pMb - pig
    
  • 1lhs – stMb – sea turtle
    
  • 1mbs – Mb - seal
    
  • 3qm5, 3qm6, [[2nrl] – btMb – blackfin tuna
    
  • 2nrm – btMb S-nitrosylated
    
  • 1mba, 3mba, 4mba – AlMb - Aplysia limacine
    
  • 1uvy – Mb – Paramecium caudatum
    

• Mb mutants uncomplexed

• • 3rgk – hMb (mutant) – human
    
  • 3m38, 3m39, 3m3a, 3m3b, 3k9z, 3h57, 3h58, 2e2y, 2ef2, 2oh8, 2oh9, 2oha, 2ohb, 2blh, 2bli, 1h1x, 1co8, 1n9h, 1n9i, 1n9x, 1naz, 1f63, 1f65, 1dti, 1co9, 1cp0, 1cp5, 1cpw, 1ch1, 1ch2, 1ch3, 1ch5, 1ch7, 1ch9, 1cik, 1cio, 1ofk, 1ofj, 102m, 1obm, 2mbw, 1tes, 1irc, 1mti, 1mtj, 1mtk, 1mlf, 1mlg, 1mlh, 1mlj, 1mlk, 1mll, 1mlm, 1mlo, 1mlr, 1mln, 1mls, 2mga, 2mgb, 2mgc, 2mgd, 2mge, 2mgf, 2mgg, 2mgh, 2mgi, 2mgj, 2mgk, 2mgl, 2mgm, 2spl, 2spm, 2spn, 2spo, 1fcs, 1j52, 1lue, 1o16, 3ogb, 3sdn, 3o89, 4fwx, 4fwz, 4it8, 4lpi, 4of9, 4ood, 4pq6, 4pqb, 4pqc, 4qau, 4tyx, 5b84, 5b85, 5c6y, 5hlq, 5ile, 5ilm, 5ilp, 5ilr, 5ut8, 5ut9, 5utb, 5utc, 5vnu, 5vrt, 5wjk, 5xkv, 5xkw, 5yzf, 5zeo, 6d45, 6jp1, 6g5t, 6g5b, 6g5a, 6f1a, 6f19, 6f18, 6f17, 5zzf - SwMb (mutant)
    
  • 2bwh - SwMb (mutant) – Laue
    
  • 3hc9, 3hen, 3heo, 3hep, 1nz2, 1nz3, 1rse, 1abs, 1xch, 1hrm, 1yma, 3rj6, 3wyo, 4ns2, 5z7f, 5z7e - hoMb (mutant) – horse
    
  • 2vlx , 2vly, 2vlz, 2vm0 – hoMb fragment
    
  • 1dm1 – AlMb (mutant)
    

• Mb containing a non-Fe protoporphyrin

• • 1yog, 1yoh, 1yoi, 1myz, 6n02, 6n03, 6mv0 – SwMb+Co protoporphyrin
    
  • 3mn0 – SwMb (mutant)+Cu protoporphyrin+cyanide
    
  • 4mxk, 4mxl - SwMb (mutant)+Zn protoporphyrin
    
  • 1j3f – SwMb+Cr salophen
    
  • 1ufj, 1ufp – SwMb (mutant)+Fe salophen
    
  • 2o58, 2o5b, 3wi8, 5yl3 – hoMb+Mn protoporphyrin
    
  • 2o5l - hoMb+Mn protoporphyrin +methanol
    
  • 2o5m - hoMb+Mn protoporphyrin +azide
    
  • 2o5o, 2o5q - hoMb+Mn protoporphyrin +NO2
    
  • 2o5s - hoMb+Co protoporphyrin +NO2
    
  • 2o5t - hoMb+Co protoporphyrin
    
  • 3wft, 3wfu - hoMb+Co tetrahydrocorrin
    
  • 5azq, 5azr - hoMb+Co tetrahydrocorrin + CN
    
  • 3rjn - hoMb+Zn deuteroporphyrin
    
  • 4twu, 4twv – hoMb (mutant) +Zn deuteroporphyrin
    

• Mb+NO

• • 1jdo, 1mlu, 5vzn – SwMb+NO
    
  • 1hjt, 5hlu, 5vzo, 5vzp, 5vzq – SwMb (mutant)+NO
    
  • 2frj, 2frk, 1npf - hoMb+NO
    
  • 2nx0 – BtMb+NO

• Mb+N2O

• • 4nxc, 5ut7 – SwMb+N2O
    
  • 5uta, 5utd, 6cf0 – SwMb (mutant) +N2O
    

• Mb+NO2

• • 2frf, 2fri, 3lr7, 3lr9, 3vau, 3v2v, 3v2z - hoMb+NO2
    
  • 5hlx – SwMb (mutant)+NO2
    

• Mb+O2

• • 1ltw, 5hav - SwMb (mutant)+O2
    
  • 1a6m, 1mbo, 2z6s, 2z6t, 6bmg – SwMb+O2
    
  • 1mno - pMb (mutant)+O2
    
  • 3vm9 - hoMb + O

• Mb+CO

• • 2bw9, 1mz0 - SwMb (mutant)+CO – Laue
    
  • 2g0r, 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12, 2g14, 2blj, 1dxc, 1dxd, 1do1, 1do3, 1do4, 1do7, 1abs, 1mcy, 1mbc, 3nml – SwMb (mutant)+CO
    
  • 1bzr , 1a6g, 1ajg, 1ajh, 1spe, 1mym, 1mbc, 5kkk – SwMb+CO
    
  • 1myf - SwMb+CO – NMR
    
  • 2mb5 - SwMb+CO – Neutron
    
  • 1dwr, 1dws, 1dwt, 5cmv – hoMb+CO
    
  • 1mdn, 1m6c – pMb (mutant)+CO
    
  • 1mwc, 1yca – pMb+CO
    
  • 3qm7 – btMb + CO

• Mb+OH

• • 1n9f – SwMb (mutant)+OH
    
  • 1gjn – hoMb+OH

• Mb+cyano compounds

• • 2jho – SwMb cyanoMet
    
  • 1ebc, 2cmm - SwMb+cyanide
    
  • 1iop – SwMb+cyanide+hemin
    
  • 108m, 101m, 104m, 105m, 2myc, 2myd, 2mya, 2mye, 2myb – SwMb+isocyanides
    
  • 103m, 107m, 111m, 106m, 109m, 110m, 112m – SwMb (mutant) +isocyanides
    
  • 6e04, 6303, 6e02 - SwMb + nitroso derivative
    
  • 5kd1 - SwMb (mutant) + nitrosoamphetamine
    
  • 3ba2 – hoMb+cyanide
    
  • 2fal – AlMb+cyanide
    
  • 2fam – AlMb+thiocyanate
    
  • 1lht – stMb+cyanide
    
  • 1emy – Mb+cyanide – asian elephant
    
  • 3qm8 - btMb cyanoMet
    

• Mb + N3

• • 3qm9 – btMb + N3

• MMb

• • 1mgn, 1duk - SwMMb
    
  • 1duo – SwMMb+methyl-imidazole
    
  • 1myg, 1myh, 1myi, 1myj, 1ymb – pMMb
    
  • 1ymc – hoSulfMMB + CN
    
  • 1myt – MMb – yellowfin tuna
    

• Other complexes of Mb

• • 3a2g – SwMb (mutant)+fluorescein
    
  • 2w6x, 2w6y - SwMb (mutant)+Xe
    
  • 2w6w - SwMb +Xe
    
  • 2eb8, 2eb9 – SwMb+Cu
    
  • 4fwy - SwMb (mutant)+ Cu
    
  • 3ase – SwMb + RuO3
    
  • 2ekt, 2eku – SwMb+methyl-depropionatehemin
    
  • 2d6c – SwMb+porphycene
    
  • 1swm, 1mbi – SwMb+imidazole
    
  • 3u3e – SwMb + phenol
    
  • 6m8f – SwMb + sucrose
    
  • 4h07, 5zzg - SwMb (mutant)+ phenol erivative
    
  • 4h0b - SwMb (mutant)+ DMSO
    
  • 1wvp – SwMb+tetrazolyl histidine
    
  • 2evk – SwMb (mutant)+acetic acid
    
  • 2evp - SwMb (mutant)+mercaptoethanol
    
  • 1v9q - SwMb (mutant)+Mn salophen derivative
    
  • 1dtm - SwMb (mutant)+4-methylimidazole
    
  • 2nsr – hoMb+nitro methane
    
  • 1npg – hoMb+nitrosoethane
    
  • 2nss - hoMb+nitro benzene
    
  • 1azi - hoMb+azide
    
  • 1bje – hoMb (mutant)+azide
    
  • 1nz4 – hoMb (mutant)+Cd
    
  • 1nz5 - hoMb (mutant)+Mn
    
  • 2in4 - hoMb+Zn-DME
    
  • 1gjn – hoMb+hydroxide
    
  • 1mni – pMb+imidazole
    
  • 3qma - btMb+imidazole
    
  • 5mba – AlMb+azide
    

• apo-Mb

• • 1bvc, 1bvd – SwApo-Mb + biliverdin

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External Resources

• Myoglobin in Wikipedia

References

1. ↑ Ordway GA, Garry DJ. Myoglobin: an essential hemoprotein in striated muscle. J Exp Biol. 2004 Sep;207(Pt 20):3441-6. PMID:15339940 doi:http://dx.doi.org/10.1242/jeb.01172