PDBsum entry 1v55

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
514 a.a. *
227 a.a. *
259 a.a. *
144 a.a. *
105 a.a. *
98 a.a. *
84 a.a. *
79 a.a. *
73 a.a. *
58 a.a. *
49 a.a. *
46 a.a. *
43 a.a. *
HEA ×4
TGL ×6
PGV ×8
CUA ×2
CHD ×8
CDL ×4
PEK ×6
UNX ×2
PSC ×2
DMU ×2
_ZN ×2
_CU ×2
_MG ×2
_NA ×2
Waters ×1943
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Bovine heart cytochromE C oxidase at the fully reduced state
Structure: CytochromE C oxidase polypeptide i. Chain: a, n. CytochromE C oxidase polypeptide ii. Chain: b, o. CytochromE C oxidase polypeptide iii. Chain: c, p. CytochromE C oxidase subunit iv isoform 1. Chain: d, q. Synonym: cox iv-1, cytochromE C oxidase polypeptide iv.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: heart. Tissue: heart
Biol. unit: 26mer (from PQS)
1.90Å     R-factor:   0.203     R-free:   0.230
Authors: T.Tsukihara,K.Shimokata,Y.Katayama,H.Shimada,K.Muramoto, H.Aoyama,M.Mochizuki,K.Shinzawa-Itoh,E.Yamashita,M.Yao, Y.Ishimura,S.Yoshikawa
Key ref:
T.Tsukihara et al. (2003). The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci U S A, 100, 15304-15309. PubMed id: 14673090 DOI: 10.1073/pnas.2635097100
21-Nov-03     Release date:   23-Dec-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1
514 a.a.
514 a.a.*
Protein chains
Pfam   ArchSchema ?
P68530  (COX2_BOVIN) -  Cytochrome c oxidase subunit 2
227 a.a.
227 a.a.*
Protein chains
Pfam   ArchSchema ?
P00415  (COX3_BOVIN) -  Cytochrome c oxidase subunit 3
261 a.a.
259 a.a.
Protein chains
Pfam   ArchSchema ?
P00423  (COX41_BOVIN) -  Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
169 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
P00426  (COX5A_BOVIN) -  Cytochrome c oxidase subunit 5A, mitochondrial
152 a.a.
105 a.a.
Protein chains
Pfam   ArchSchema ?
P00428  (COX5B_BOVIN) -  Cytochrome c oxidase subunit 5B, mitochondrial
129 a.a.
98 a.a.
Protein chains
Pfam   ArchSchema ?
P07471  (CX6A2_BOVIN) -  Cytochrome c oxidase subunit 6A2, mitochondrial
97 a.a.
84 a.a.*
Protein chains
Pfam   ArchSchema ?
P00429  (CX6B1_BOVIN) -  Cytochrome c oxidase subunit 6B1
86 a.a.
79 a.a.
Protein chains
Pfam   ArchSchema ?
P04038  (COX6C_BOVIN) -  Cytochrome c oxidase subunit 6C
74 a.a.
73 a.a.*
Protein chains
Pfam   ArchSchema ?
P07470  (CX7A1_BOVIN) -  Cytochrome c oxidase subunit 7A1, mitochondrial
80 a.a.
58 a.a.
Protein chains
Pfam   ArchSchema ?
P13183  (COX7B_BOVIN) -  Cytochrome c oxidase subunit 7B, mitochondrial
80 a.a.
49 a.a.
Protein chains
Pfam   ArchSchema ?
P00430  (COX7C_BOVIN) -  Cytochrome c oxidase subunit 7C, mitochondrial
63 a.a.
46 a.a.
Protein chains
Pfam   ArchSchema ?
P10175  (COX8B_BOVIN) -  Cytochrome c oxidase subunit 8B, mitochondrial
70 a.a.
43 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, N: E.C.  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = HEA)
matches with 50.00% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Copper
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   10 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     electron carrier activity     8 terms  


DOI no: 10.1073/pnas.2635097100 Proc Natl Acad Sci U S A 100:15304-15309 (2003)
PubMed id: 14673090  
The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa.
Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. We report that the Asp-51 --> Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Improved x-ray structures (at 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggests that the channel functions as an effective proton-collecting region. Infrared results indicate that the conformation of Asp-51 is controlled only by the oxidation state of the low-spin heme. These results indicate that the low-spin heme drives the proton-pumping process.
  Selected figure(s)  
Figure 2.
Fig. 2. Redox-coupled conformational changes in Asp-51. (A) Stereoscopic drawing of the hydrogen-bond network in the fully oxidized and reduced (blue structure) states at 1.8- and 1.9-Å resolution, respectively, viewed from the intermembrane side. The two histidines bound to Fe[a] (heme a iron), are not shown. (B) The hydrogen-bonding structure of Asp-51 in the oxidized (Left) and reduced (Right) states. The smooth thick curve denotes the molecular surface to which the water molecules in the intermembrane space are accessible. The conformational changes induced by reduction of the enzyme are shown by blue structures in Right. The blue (A) and black (B) balls represent the fixed water molecules. The dotted lines denote hydrogen bonds. The double-headed dotted arrows show a possible movement of the water molecule from Arg-38 to Tyr-371.
Figure 4.
Fig. 4. Proposed proton-pumping mechanism. The iron, porphyrin, and formyl side group of heme a are shown by Fe[a], Pr, and CHO, respectively. The COOH on Pr denotes one of the propionate groups of heme a. The brackets ([]1+ and[]0) indicate the net charge of the six-coordinated heme a. The diagrams shadowed and in the dotted squares show the structures in the stable and intermediate states, respectively. The thick arrows in a and d-f and the thin arrows in d and e indicate the electrostatic influence of the net positive charge of heme a and the proton transfers upon heme a oxidation, respectively. The dotted lines in the diagrams denote the hydrogen bond network connecting Arg-38 with Asp-51, including the peptide bond that blocks the reverse proton transfer from the intermembrane side.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286652 A.V.Dyuba, A.M.Arutyunyan, T.V.Vygodina, N.V.Azarkina, A.V.Kalinovich, Y.A.Sharonov, and A.A.Konstantinov (2011).
Circular dichroism spectra of cytochrome c oxidase.
  Metallomics, 3, 417-432.  
  21253496 R.D.Koilkonda, and J.Guy (2011).
Leber's Hereditary Optic Neuropathy-Gene Therapy: From Benchtop to Bedside.
  J Ophthalmol, 2011, 179412.  
21545285 S.Yoshikawa, K.Muramoto, and K.Shinzawa-Itoh (2011).
Proton-pumping mechanism of cytochrome C oxidase.
  Annu Rev Biophys, 40, 205-223.  
20037139 D.Parul, G.Palmer, and M.Fabian (2010).
Ligand trapping by cytochrome c oxidase: implications for gating at the catalytic center.
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19835954 I.Lee, A.Pecinova, P.Pecina, B.G.Neel, T.Araki, R.Kucherlapati, A.E.Roberts, and M.Hüttemann (2010).
A suggested role for mitochondria in Noonan syndrome.
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20385840 K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, and S.Yoshikawa (2010).
Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate.
  Proc Natl Acad Sci U S A, 107, 7740-7745.
PDB codes: 3ag1 3ag2 3ag3 3ag4
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20192226 S.A.Siletsky, J.Zhu, R.B.Gennis, and A.A.Konstantinov (2010).
Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel.
  Biochemistry, 49, 3060-3073.  
21106766 V.R.Kaila, M.P.Johansson, D.Sundholm, and M.Wikström (2010).
Interheme electron tunneling in cytochrome c oxidase.
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20373004 Y.Katayama, K.Shimokata, M.Suematsu, T.Ogura, T.Tsukihara, S.Yoshikawa, and H.Shimada (2010).
Cell-free synthesis of cytochrome c oxidase, a multicomponent membrane protein.
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20396396 Y.Yoshioka, and M.Mitani (2010).
B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases.
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19303362 B.Kadenbach, R.Ramzan, and S.Vogt (2009).
Degenerative diseases, oxidative stress and cytochrome c oxidase function.
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19140675 B.Liu, Y.Chen, T.Doukov, S.M.Soltis, C.D.Stout, and J.A.Fee (2009).
Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.
  Biochemistry, 48, 820-826.
PDB codes: 3eh3 3eh4 3eh5
19432984 E.Willerslev, M.Gilbert, J.Binladen, S.Ho, P.Campos, A.Ratan, L.Tomsho, R.da Fonseca, A.Sher, T.Kuznetsova, M.Nowak-Kemp, T.Roth, W.Miller, and S.Schuster (2009).
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.
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19164527 H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, and S.Yoshikawa (2009).
A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.
  Proc Natl Acad Sci U S A, 106, 2165-2169.
PDB codes: 2zxw 3abl 3abm
19575527 H.J.Lee, L.Ojemyr, A.Vakkasoglu, P.Brzezinski, and R.B.Gennis (2009).
Properties of Arg481 mutants of the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides suggest that neither R481 nor the nearby D-propionate of heme a3 is likely to be the proton loading site of the proton pump.
  Biochemistry, 48, 7123-7131.  
19256628 I.V.Leontyev, and A.A.Stuchebrukhov (2009).
Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models.
  J Chem Phys, 130, 085103.  
19397279 L.Qin, J.Liu, D.A.Mills, D.A.Proshlyakov, C.Hiser, and S.Ferguson-Miller (2009).
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
  Biochemistry, 48, 5121-5130.
PDB codes: 3fye 3fyi
19463779 T.Egawa, H.J.Lee, R.B.Gennis, S.R.Yeh, and D.L.Rousseau (2009).
Critical structural role of R481 in cytochrome c oxidase from Rhodobacter sphaeroides.
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19666617 Y.C.Kim, M.Wikström, and G.Hummer (2009).
Kinetic gating of the proton pump in cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 106, 13707-13712.  
18798008 F.M.Ho (2008).
Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems.
  Photosynth Res, 98, 503-522.  
17949262 I.Belevich, and M.I.Verkhovsky (2008).
Molecular mechanism of proton translocation by cytochrome C oxidase.
  Antioxid Redox Signal, 10, 1.  
18155154 J.Xu, and G.A.Voth (2008).
Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.
  Biochim Biophys Acta, 1777, 196-201.  
18843528 M.Hüttemann, I.Lee, A.Pecinova, P.Pecina, K.Przyklenk, and J.W.Doan (2008).
Regulation of oxidative phosphorylation, the mitochondrial membrane potential, and their role in human disease.
  J Bioenerg Biomembr, 40, 445-456.  
17876762 M.P.Johansson, V.R.Kaila, and L.Laakkonen (2008).
Charge parameterization of the metal centers in cytochrome c oxidase.
  J Comput Chem, 29, 753-767.  
18320260 R.G.Melvin, S.D.Katewa, and J.W.Ballard (2008).
A candidate complex approach to study functional mitochondrial DNA changes: sequence variation and quaternary structure modeling of Drosophila simulans cytochrome c oxidase.
  J Mol Evol, 66, 232-242.  
18318906 R.R.da Fonseca, W.E.Johnson, S.J.O'Brien, M.J.Ramos, and A.Antunes (2008).
The adaptive evolution of the mammalian mitochondrial genome.
  BMC Genomics, 9, 119.  
18541140 R.Sugitani, E.S.Medvedev, and A.A.Stuchebrukhov (2008).
Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme.
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18953727 S.Gupta, and S.Mazumdar (2008).
Inhibition of bacterial oxidases by formamide and analogs.
  Biol Chem, 389, 599-607.  
18493604 T.A.Castoe, Z.J.Jiang, W.Gu, Z.O.Wang, and D.D.Pollock (2008).
Adaptive evolution and functional redesign of core metabolic proteins in snakes.
  PLoS ONE, 3, e2201.  
18430799 V.R.Kaila, M.I.Verkhovsky, G.Hummer, and M.Wikström (2008).
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 105, 6255-6259.  
17923475 D.J.Mancuso, H.F.Sims, X.Han, C.M.Jenkins, S.P.Guan, K.Yang, S.H.Moon, T.Pietka, N.A.Abumrad, P.H.Schlesinger, and R.W.Gross (2007).
Genetic ablation of calcium-independent phospholipase A2gamma leads to alterations in mitochondrial lipid metabolism and function resulting in a deficient mitochondrial bioenergetic phenotype.
  J Biol Chem, 282, 34611-34622.  
17293458 I.Belevich, D.A.Bloch, N.Belevich, M.Wikström, and M.I.Verkhovsky (2007).
Exploring the proton pump mechanism of cytochrome c oxidase in real time.
  Proc Natl Acad Sci U S A, 104, 2685-2690.  
17470809 K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-o, E.Yamashita, H.Aoyama, T.Tsukihara, and S.Yoshikawa (2007).
A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 104, 7881-7886.
PDB codes: 2eij 2eik 2eil 2eim 2ein
17360500 K.Shimokata, Y.Katayama, H.Murayama, M.Suematsu, T.Tsukihara, K.Muramoto, H.Aoyama, S.Yoshikawa, and H.Shimada (2007).
The proton pumping pathway of bovine heart cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 104, 4200-4205.  
17332748 K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, and S.Yoshikawa (2007).
Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase.
  EMBO J, 26, 1713-1725.
PDB codes: 2dyr 2dys
18240421 M.Hüttemann, I.Lee, L.Samavati, H.Yu, and J.W.Doan (2007).
Regulation of mitochondrial oxidative phosphorylation through cell signaling.
  Biochim Biophys Acta, 1773, 1701-1720.  
17239857 P.Lemma-Gray, S.T.Weintraub, C.A.Carroll, A.Musatov, and N.C.Robinson (2007).
Tryptophan 334 oxidation in bovine cytochrome c oxidase subunit I involves free radical migration.
  FEBS Lett, 581, 437-442.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
17287344 Y.C.Kim, M.Wikström, and G.Hummer (2007).
Kinetic models of redox-coupled proton pumping.
  Proc Natl Acad Sci U S A, 104, 2169-2174.  
16814104 A.Musatov (2006).
Contribution of peroxidized cardiolipin to inactivation of bovine heart cytochrome c oxidase.
  Free Radic Biol Med, 41, 238-246.  
16761090 D.M.Popovic, and A.A.Stuchebrukhov (2006).
Two conformational states of Glu242 and pKas in bovine cytochrome c oxidase.
  Photochem Photobiol Sci, 5, 611-620.  
16411750 E.Sedlák, M.Panda, M.P.Dale, S.T.Weintraub, and N.C.Robinson (2006).
Photolabeling of cardiolipin binding subunits within bovine heart cytochrome c oxidase.
  Biochemistry, 45, 746-754.  
16598262 I.Belevich, M.I.Verkhovsky, and M.Wikström (2006).
Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase.
  Nature, 440, 829-832.  
16756489 J.P.Hosler, S.Ferguson-Miller, and D.A.Mills (2006).
Energy transduction: proton transfer through the respiratory complexes.
  Annu Rev Biochem, 75, 165-187.  
16419070 L.Adamian, and J.Liang (2006).
Prediction of buried helices in multispan alpha helical membrane proteins.
  Proteins, 63, 1-5.  
17203431 L.Laakkonen, R.W.Jobson, and V.A.Albert (2006).
A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power.
  Plant Biol (Stuttg), 8, 758-764.  
17050688 L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, and S.Ferguson-Miller (2006).
Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 103, 16117-16122.
PDB code: 2gsm
16788913 M.R.Blomberg, and P.E.Siegbahn (2006).
Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case.
  J Comput Chem, 27, 1373-1384.  
16842995 P.Brzezinski, and P.Adelroth (2006).
Design principles of proton-pumping haem-copper oxidases.
  Curr Opin Struct Biol, 16, 465-472.  
16641489 T.Páli, D.Bashtovyy, and D.Marsh (2006).
Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures.
  Protein Sci, 15, 1153-1161.  
15770678 Grey (2005).
Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity?
  Bioessays, 27, 436-446.  
15653739 B.Nie, J.Stutzman, and A.Xie (2005).
A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.
  Biophys J, 88, 2833-2847.  
15999422 C.Abad-Zapatero, and M.G.Replacement (2005).
Homage to Prof. M.G. Replacement: a celebration of structural biology at Purdue University.
  Structure, 13, 845-848.  
16148937 K.Faxén, G.Gilderson, P.Adelroth, and P.Brzezinski (2005).
A mechanistic principle for proton pumping by cytochrome c oxidase.
  Nature, 437, 286-289.  
16014708 M.Wikström, C.Ribacka, M.Molin, L.Laakkonen, M.Verkhovsky, and A.Puustinen (2005).
Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase.
  Proc Natl Acad Sci U S A, 102, 10478-10481.  
15949761 P.K.Fyfe, A.V.Hughes, P.Heathcote, and M.R.Jones (2005).
Proteins, chlorophylls and lipids: X-ray analysis of a three-way relationship.
  Trends Plant Sci, 10, 275-282.  
15798371 S.J.Zullo, W.T.Parks, M.Chloupkova, B.Wei, H.Weiner, W.A.Fenton, J.M.Eisenstadt, and C.R.Merril (2005).
Stable transformation of CHO Cells and human NARP cybrids confers oligomycin resistance (oli(r)) following transfer of a mitochondrial DNA-encoded oli(r) ATPase6 gene to the nuclear genome: a model system for mtDNA gene therapy.
  Rejuvenation Res, 8, 18-28.  
15807657 S.Papa (2005).
Role of cooperative H(+)/e(-) linkage (redox bohr effect) at heme a/Cu(A) and heme a(3)/Cu(B) in the proton pump of cytochrome c oxidase.
  Biochemistry (Mosc), 70, 178-186.  
15865995 Z.O.Wang, and D.D.Pollock (2005).
Context dependence and coevolution among amino acid residues in proteins.
  Methods Enzymol, 395, 779-790.  
15326290 H.J.Hwang, and Y.Lu (2004).
pH-dependent transition between delocalized and trapped valence states of a CuA center and its possible role in proton-coupled electron transfer.
  Proc Natl Acad Sci U S A, 101, 12842-12847.  
15289603 L.Salomonsson, A.Lee, R.B.Gennis, and P.Brzezinski (2004).
A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter.
  Proc Natl Acad Sci U S A, 101, 11617-11621.  
15236746 P.Brzezinski (2004).
Redox-driven membrane-bound proton pumps.
  Trends Biochem Sci, 29, 380-387.  
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 codes are shown on the right.