• Protein Explorer home page (maintained at molvis.sdsc.edu).  Here is a link to a PDB-Lite Search Site.

Methylamine Dehydrogenase:Amicyanin:Cytochrome c_551i ternary complex

• 2mta: L.Chen, R.C.E. Durley, F.S.Mathews, V.L.Davidson  STRUCTURE OF AN ELECTRON TRANSFER COMPLEX: METHYLAMINE DEHYDROGENASE, AMICYANIN, AND CYTOCHROME C551I Science 1994, 264, 86-90. (resolution 2.4 Å)

Complex II

• 1qla: Respiratory Complex II-Like Fumarate Reductase From Wolinella Succinogenes  C.R.D.Lancaster, A.Kroeger, M.Auer, H.Michel  STRUCTURE OF FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES AT 2.2 ANGSTROMS RESOLUTION Nature 1999, 402, 377.

Cytochrome bc1 complex (complex III)

• 1be3: Cytochrome Bc1 Complex From Bovine  S.Iwata, J.W.Lee, K.Okada, J.K.Lee, M.Iwata, B.Rasmussen, T.A.Link, S.Ramaswamy, B.K.Jap (COMPLETE STRUCTURE OF THE 11-SUBUNIT BOVINE MITOCHONDRIAL CYTOCHROME BC1 COMPLEX, Science 1998, 281, 64).  Resolution=3.0 Å.  The structure 1be3 is the P 6₅22 space group structure; the complex is a dimer, but only one-half of the dimer is shown since the other half is related by symmetry.
• A second structure (1bgy) is reported in the same paper, with slightly different conformations.  This structure is in space group  P 6₅ and the two halves of the dimer are not related by symmetry, so this structure can be used to see the dimeric interaction.  This structure also has resolution=3.0 Å.
• 1bcc: Cytochrome Bc1 Complex From Chicken  Z.Zhang, L.Huang, V.M.Shulmeister, Y.-I.Chi, K.K.Kim, L.-W.Hung, A.R.Crofts, E.A.Berry, S.-H.Kim ELECTRON TRANSFER BY DOMAIN MOVEMENT IN CYTOCHROME BC1 Nature1998, 392, 677.  (resolution 3.16 Å)
• 3bcc: Stigmatellin And Antimycin Bound Cytochrome Bc1 Complex From Chicken  Z.Zhang, L.Huang, V.M.Shulmeister, Y.I.Chi, K.K.Kim, L.W.Hung, A.R.Crofts, E.A.Berry, S.H.Kim  ELECTRON TRANSFER BY DOMAIN MOVEMENT IN CYTOCHROME BC1 Nature1998, 392, 677.  (resolution 3.7 Å)
• 2bcc: Stigmatellin Bound Cytochrome Bc1 Complex From Chicken  Z.Zhang, L.Huang, V.M.Shulmeister, Y.-I.Chi, K.K.Kim, L.-W.Hung, A.R.Crofts, E.A.Berry, S.-H.Kim

Cytochrome c oxidase (complex IV)

• 2occ: Bovine Heart Cytochrome C Oxidase At The Fully Oxidized State (1998 structure at 2.3 Å resolution).  submitted by T.TSUKIHARA,M.YAO. Journal references are S.YOSHIKAWA, K.SHINZAWA-ITOH, R.NAKASHIMA, R.YAONO, E.YAMASHITA, N.INOUE, M.YAO, M.J.FEI, C.P.LIBEU, T.MIZUSHIMA, H.YAMAGUCHI, T.TOMIZAKI, T.TSUKIHARA "REDOX-COUPLED CRYSTAL STRUCTURAL CHANGES IN BOVINE HEART CYTOCHROME C OXIDASE", Science 1998, 280, 1723.  T.TSUKIHARA, H.AOYAMA, E.YAMASHITA, T.TOMIZAKI, H.YAMAGUCHI, K.SHINZAWA-ITOH, R.NAKASHIMA, R.YAONO, S.YOSHIKAWA "THE WHOLE STRUCTURE OF THE 13-SUBUNIT OXIDIZED CYTOCHROME C OXIDASE AT 2.8 A Science 1996, 272, 1136. Same authors,  STRUCTURES OF METAL SITES OF OXIDIZED BOVINE HEART CYTOCHROME C OXIDASE AT 2.8 A  Science 1996, 269, 1069.  Also available is the carbon monoxide bound form (1oco), reduced state (1ocr) and azide bound form (1ocz).

Photosynthesis

• 1prc: Photosynthetic Reaction Center from Rhodopseudomonas Viridis.  A 1994 submission at 2.3 Å resolution.  The publication of a lower resolution structure in 1985 led to a Nobel Prize in 1989. J.Deisenhofer, O.Epp, I.Sinning, H.Michel STRUCTURE OF THE PROTEIN SUBUNITS IN THE PHOTOSYNTHETIC REACTION CENTRE OF RHODOPSEUDOMONAS VIRIDIS AT 3 ANGSTROMS RESOLUTION Nature, 1985, 318, 618.
• 1c51: Photosynthetic Reaction Center And Core Antenna System (Trimeric), Alpha Carbon Only O.Klukas, W.-D.Schubert, P.Jordan, N.Krauss, P.Fromme, H.T.Witt, W.Saenger PHOTOSYSTEM I, AN IMPROVED MODEL OF THE STROMAL SUBUNITS PSAC, PSAD AND PSAE  J. Biol. Chem.1999, 274, 7351. (4.0 Å resolution)
• Click here for a CHIME (not PE) presentation on a bacterial light harvesting complex put together by Antony Crofts, University of Illinois at Urbana-Champaign.  The literature reference is McDermott, G, Prince, S.M., Freer, A.A., Hawthornthwaite-Lawless, A.M., Papiz, M.Z., Cogdell, R.J. and Isaacs, N.W. "Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria." Nature 1995 374, 517-521.

ATP Synthase

• 1c17: Model of ac(12) of F0 (membrane bound) subunits of ATP synthase.  A 1999 structure based on solution NMR data.  Modelled data as ac₁₂.  Rastogi, V. K.; Girvin, M. E "Structural Changes Linked to Proton Translocation by Subunit c of the ATP Synthase" Nature, 1999, 402, 263.
• Comparison of 1c0v vs. 1c99 shows how structure of c subunit when Asp 61 is protonated (top) or deptrotonated (bottom).  If you wish to look at these structures one at a time, use the following links: 1c0v: Structure of c subunit when Asp61 is protonated.  Girvin, M. E.; Rastogi, V. K.; Abildgaard, F.; Markley, J. L.; Fillingame, R. H. "Solution Structure of the Transmembrane H+-transporting Subunit C of the F1F0 ATP Synthase" Biochemistry, 1998, 37, 8817. and 1c99: Structure of c subunit when Asp61 is deprotonated (from the 1999 Nature paper cited above)

Some enzymes

• 2sbl: Soybean lipoxygenase-1.
• Nitrile hydratase, a non-heme iron containing enzyme that converts nitriles to amides.  Found in soil- bacteria and expressed at high levels in soils contaminated by acetonitrile, etc.  Has been used for "green" synthesis of acrylamide and the pain-reliever naproxen.  The enzyme isolated from bacteria grown in the dark is inactive and has nitric oxide (NO) bound to the active site; this can be displaced by exposure to light.  Two crystal structures are available.  The light form (1ahj; Nitrile Hydratase; W.Huang, J.Jia, J.Cummings, M.Nelson, G.Schneider, Y.Lindqvist) is at relatively low resolution (2.65 Å), while the resolution of the dark form (2ahj; Nitrile Hydratase Complexed With Nitric Oxide; S.Nagashima, M.Nakasako, N.Dohmae, M.Tsujimura, K.Takio, M.Odaka, M.Yohda, N.Kamiya, I.Endo) is much better (1.7 Å).  One question that has not yet been established definitively is whether the three oxygen atoms bound to two of the sulfur ligand atoms in the dark form are also present in the active form of the enzyme, although a reasonable presumption is that these two cysteine ligands are oxididized in the active form, but the oxygens were not found because of the lower resolution of the light form structure.