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PDBsum entry 1vry
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Membrane protein PDB id
1vry

 

 

 

 

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Contents
Protein chain
61 a.a. *
* Residue conservation analysis
PDB id:
1vry
Name: Membrane protein
Title: Second and third transmembrane domains of the alpha-1 subunit of human glycine receptor
Structure: Glycine receptor alpha-1 chain. Chain: a. Fragment: second and third transmembrane domains. Synonym: glycine receptor 48 kda subunit, strychnine binding subunit. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: glra1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 20 models
Authors: D.Ma,Z.Liu,L.Li,P.Tang,Y.Xu
Key ref:
D.Ma et al. (2005). Structure and dynamics of the second and third transmembrane domains of human glycine receptor. Biochemistry, 44, 8790-8800. PubMed id: 15952785 DOI: 10.1021/bi050256n
Date:
20-Jul-05     Release date:   26-Jul-05    
Supersedes: 1zhd
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23415  (GLRA1_HUMAN) -  Glycine receptor subunit alpha-1 from Homo sapiens
Seq:
Struc: 		457 a.a.
61 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1021/bi050256n Biochemistry 44:8790-8800 (2005)
PubMed id: 15952785  
 
 
Structure and dynamics of the second and third transmembrane domains of human glycine receptor.
D.Ma, Z.Liu, L.Li, P.Tang, Y.Xu.
 
  ABSTRACT  
 
A 61-residue polypeptide resembling the second and third transmembrane domains (TM23) of the alpha-1 subunit of human glycine receptor and its truncated form, both with the wild-type loop linking the two TM domains (the "23" loop), were studied using high-resolution NMR. Well-defined domain structures can be identified for the TM2, 23 loop, and TM3 regions. Contrary to the popular model of a long and straight alpha-helical structure for the pore-lining TM2 domain for the Cys-loop receptor family, the last three residues of the TM2 domain and the first eight residues of the 23 loop (S16-S26) seem to be intrinsically nonhelical and highly flexible even in trifluoroethanol, a solvent known to promote and stabilize alpha-helical structures. The six remaining residues of the 23 loop and most of the TM3 domain exhibit helical structures with a kinked pi-helix (or a pi-turn) from W34 to C38 and a kink angle of 159 +/- 3 degrees . The tertiary fold of TM3 relative to TM2 is defined by several unambiguously identified long-range NOE cross-peaks within the loop region and between TM2 and TM3 domains. The 20 lowest-energy structures show a left-handed tilt of TM3 relative to TM2 with a tilting angle of 44 +/- 2 degrees between TM2 (V1-Q14) and TM3 (L39-E48) helix axes. This left-handed TM2-TM3 arrangement ensures a neatly packed right-handed quaternary structure of five subunits to form an ion-conducting pore. This is the first time that two TM domains of the glycine receptor linked by the important 23 loop have ever been analyzed at atomistic resolution. Many structural characteristics of the receptor can be inferred from the structural and dynamical features identified in this study.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460829 W.Xiong, K.Cheng, T.Cui, G.Godlewski, K.C.Rice, Y.Xu, and L.Zhang (2011).
Cannabinoid potentiation of glycine receptors contributes to cannabis-induced analgesia.
  Nat Chem Biol, 7, 296-303.  
20849671 A.J.Thompson, H.A.Lester, and S.C.Lummis (2010).
The structural basis of function in Cys-loop receptors.
  Q Rev Biophys, 43, 449-499.  
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
  20161395 H.J.Kim, S.C.Howell, W.D.Van Horn, Y.H.Jeon, and C.R.Sanders (2009).
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins.
  Prog Nucl Magn Reson Spectrosc, 55, 335-360.  
19427904 J.A.Paulo, and E.Hawrot (2009).
Effect of homologous serotonin receptor loop substitutions on the heterologous expression in Pichia of a chimeric acetylcholine-binding protein with alpha-bungarotoxin-binding activity.
  Protein Expr Purif, 67, 76-81.  
  19177358 R.C.Page, S.Lee, J.D.Moore, S.J.Opella, and T.A.Cross (2009).
Backbone structure of a small helical integral membrane protein: A unique structural characterization.
  Protein Sci, 18, 134-146.
PDB code: 2k3m
18788737 C.G.Canlas, D.Ma, P.Tang, and Y.Xu (2008).
Residual dipolar coupling measurements of transmembrane proteins using aligned low-q bicelles and high-resolution magic angle spinning NMR spectroscopy.
  J Am Chem Soc, 130, 13294-13300.  
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.  
18310240 D.Ma, N.R.Brandon, T.Cui, V.Bondarenko, C.Canlas, J.S.Johansson, P.Tang, and Y.Xu (2008).
Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses.
  Biophys J, 94, 4454-4463.
PDB code: 2i7u
18043720 K.Becker, H.G.Breitinger, A.Humeny, H.M.Meinck, B.Dietz, F.Aksu, and C.M.Becker (2008).
The novel hyperekplexia allele GLRA1(S267N) affects the ethanol site of the glycine receptor.
  Eur J Hum Genet, 16, 223-228.  
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.  
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.  
18762867 S.C.Shih, I.Stoica, and N.K.Goto (2008).
Investigation of the utility of selective methyl protonation for determination of membrane protein structures.
  J Biomol NMR, 42, 49-58.  
17893361 J.Hu, H.Qin, C.Li, M.Sharma, T.A.Cross, and F.P.Gao (2007).
Structural biology of transmembrane domains: efficient production and characterization of transmembrane peptides by NMR.
  Protein Sci, 16, 2153-2165.  
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
16826539 C.R.Sanders, and F.Sönnichsen (2006).
Solution NMR of membrane proteins: practice and challenges.
  Magn Reson Chem, 44, S24-S40.  
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.  
16387778 J.M.Johnston, G.A.Cook, J.M.Tomich, and M.S.Sansom (2006).
Conformation and environment of channel-forming peptides: a simulation study.
  Biophys J, 90, 1855-1864.  
17176085 J.Song, M.S.Lee, I.Carlberg, A.V.Vener, and J.L.Markley (2006).
Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications.
  Biochemistry, 45, 15633-15643.
PDB code: 2fft
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 code is shown on the right.

 

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