PDBsum entry 1l0m

Go to PDB code: 
protein links
Proton transport PDB id
Protein chain
212 a.a. *
* Residue conservation analysis
PDB id:
Name: Proton transport
Title: Solution structure of bacteriorhodopsin
Structure: Bacteriorhodopsin. Chain: a. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: the peptide, corresponding to different secondary structure elements, was chemically synthesized. The sequence of this peptide is naturally found in halobacterium halobium.
NMR struc: 1 models
Authors: M.Katragadda,J.L.Alderfer,P.L.Yeagle
Key ref: M.Katragadda et al. (2001). Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin. Biophys J, 81, 1029-1036. PubMed id: 11463644
11-Feb-02     Release date:   27-Mar-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02945  (BACR_HALSA) -  Bacteriorhodopsin
262 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


Biophys J 81:1029-1036 (2001)
PubMed id: 11463644  
Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin.
M.Katragadda, J.L.Alderfer, P.L.Yeagle.
Three-dimensional structures of only a handful of membrane proteins have been solved, in contrast to the thousands of structures of water-soluble proteins. Difficulties in crystallization have inhibited the determination of the three-dimensional structure of membrane proteins by x-ray crystallography and have spotlighted the critical need for alternative approaches to membrane protein structure. A new approach to the three-dimensional structure of membrane proteins has been developed and tested on the integral membrane protein, bacteriorhodopsin, the crystal structure of which had previously been determined. An overlapping series of 13 peptides, spanning the entire sequence of bacteriorhodopsin, was synthesized, and the structures of these peptides were determined by NMR in dimethylsulfoxide solution. These structures were assembled into a three-dimensional construct by superimposing the overlapping sequences at the ends of each peptide. Onto this construct were written all the distance and angle constraints obtained from the individual solution structures along with a limited number of experimental inter-helical distance constraints, and the construct was subjected to simulated annealing. A three-dimensional structure, determined exclusively by the experimental constraints, emerged that was similar to the crystal structure of this protein. This result suggests an alternative approach to the acquisition of structural information for membrane proteins consisting of helical bundles.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21455270 B.L.Lee, B.D.Sykes, and L.Fliegel (2011).
Structural analysis of the Na+/H+ exchanger isoform 1 (NHE1) using the divide and conquer approach.
  Biochem Cell Biol, 89, 189-199.  
21337621 S.Hwang, and C.Hilty (2011).
Folding determinants of disulfide bond forming protein B explored by solution nuclear magnetic resonance spectroscopy.
  Proteins, 79, 1365-1375.
PDB codes: 2l0l 2l0m 2l0n 2l0o
19383463 A.Neumoin, L.S.Cohen, B.Arshava, S.Tantry, J.M.Becker, O.Zerbe, and F.Naider (2009).
Structure of a double transmembrane fragment of a G-protein-coupled receptor in micelles.
  Biophys J, 96, 3187-3196.
PDB code: 2k9p
19176522 B.L.Lee, X.Li, Y.Liu, B.D.Sykes, and L.Fliegel (2009).
Structural and Functional Analysis of Transmembrane XI of the NHE1 Isoform of the Na+/H+ Exchanger.
  J Biol Chem, 284, 11546-11556.
PDB code: 2kbv
18937032 C.Zou, F.Naider, and O.Zerbe (2008).
Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.
  J Biomol NMR, 42, 257-269.  
18260136 L.S.Cohen, B.Arshava, R.Estephan, J.Englander, H.Kim, M.Hauser, O.Zerbe, M.Ceruso, J.M.Becker, and F.Naider (2008).
Expression and biophysical analysis of two double-transmembrane domain-containing fragments from a yeast G protein-coupled receptor.
  Biopolymers, 90, 117-130.  
18177734 M.Musial-Siwek, D.A.Kendall, and P.L.Yeagle (2008).
Solution NMR of signal peptidase, a membrane protein.
  Biochim Biophys Acta, 1778, 937-944.  
18178144 O.Y.Dmitriev, K.H.Freedman, J.Hermolin, and R.H.Fillingame (2008).
Interaction of transmembrane helices in ATP synthase subunit a in solution as revealed by spin label difference NMR.
  Biochim Biophys Acta, 1777, 227-237.  
17449670 A.Neumoin, B.Arshava, J.Becker, O.Zerbe, and F.Naider (2007).
NMR studies in dodecylphosphocholine of a fragment containing the seventh transmembrane helix of a G-protein-coupled receptor from Saccharomyces cerevisiae.
  Biophys J, 93, 467-482.  
17766379 O.Y.Dmitriev, and R.H.Fillingame (2007).
The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c.
  Protein Sci, 16, 2118-2122.  
17142275 V.Bondarenko, Y.Xu, and P.Tang (2007).
Structure of the first transmembrane domain of the neuronal acetylcholine receptor beta2 subunit.
  Biophys J, 92, 1616-1622.
PDB code: 2k58
16634087 H.Zheng, J.Zhao, W.Sheng, and X.Q.Xie (2006).
A transmembrane helix-bundle from G-protein coupled receptor CB2: biosynthesis, purification, and NMR characterization.
  Biopolymers, 83, 46-61.  
17215879 J.K.Rainey, L.Fliegel, and B.D.Sykes (2006).
Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides.
  Biochem Cell Biol, 84, 918-929.  
17131294 P.Cano-Sanchez, B.Severino, V.V.Sureshbabu, J.Russo, T.Inui, F.X.Ding, B.Arshava, J.Becker, and F.Naider (2006).
Effects of N- and C-terminal addition of oligolysines or native loop residues on the biophysical properties of transmembrane domain peptides from a G-protein coupled receptor.
  J Pept Sci, 12, 808-822.  
15622547 F.Naider, S.Khare, B.Arshava, B.Severino, J.Russo, J.M.Becker, and M.Goodman (2005).
Synthetic peptides as probes for conformational preferences of domains of membrane receptors.
  Biopolymers, 80, 199-213.  
15054892 F.Naider, R.Estephan, J.Englander, V.V.Suresh Babu, E.Arevalo, K.Samples, and J.M.Becker (2004).
Sexual conjugation in yeast: A paradigm to study G-protein-coupled receptor domain structure.
  Biopolymers, 76, 119-128.  
14517901 E.Arevalo, R.Estephan, J.Madeo, B.Arshava, M.Dumont, J.M.Becker, and F.Naider (2003).
Biosynthesis and biophysical analysis of domains of a yeast G protein-coupled receptor.
  Biopolymers, 71, 516-531.  
12725244 G.Nicastro, F.Peri, L.Franzoni, Chiara, G.Sartor, and A.Spisni (2003).
Conformational features of a synthetic model of the first extracellular loop of the angiotensin II AT1A receptor.
  J Pept Sci, 9, 229-243.  
12044163 G.Choi, J.Landin, J.F.Galan, R.R.Birge, A.D.Albert, and P.L.Yeagle (2002).
Structural studies of metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin.
  Biochemistry, 41, 7318-7324.
PDB code: 1ln6
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.