PDBsum entry 2etc

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Transport protein PDB id
Protein chains
252 a.a. *
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Crystal structure of the ankyrin repeat domain of trpv2
Structure: Transient receptor potential cation channel subfamily v member 2. Chain: a, b. Fragment: residues 62-326. Synonym: trpv2, osm-9-like trp channel 2, otrpc2, vanilloid receptor-like protein 1, vrl-1, stretch- activated channel 2b. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: trpv2, sac2b, vrl1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
3.10Å     R-factor:   0.215     R-free:   0.262
Authors: X.Jin,R.Gaudet
Key ref:
X.Jin et al. (2006). Structure of the N-terminal ankyrin repeat domain of the TRPV2 ion channel. J Biol Chem, 281, 25006-25010. PubMed id: 16809337 DOI: 10.1074/jbc.C600153200
27-Oct-05     Release date:   27-Jun-06    
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Protein chains
Pfam   ArchSchema ?
Q9WUD2  (TRPV2_RAT) -  Transient receptor potential cation channel subfamily V member 2
761 a.a.
252 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   3 terms 
  Biological process     ion transport   3 terms 
  Biochemical function     ion channel activity     1 term  


DOI no: 10.1074/jbc.C600153200 J Biol Chem 281:25006-25010 (2006)
PubMed id: 16809337  
Structure of the N-terminal ankyrin repeat domain of the TRPV2 ion channel.
X.Jin, J.Touhey, R.Gaudet.
The TRPV ion channels mediate responses to many sensory stimuli including heat, low pH, neuropeptides, and chemical ligands. All TRPV subfamily members contain an intracellular N-terminal ankyrin repeat domain (ARD), a prevalent protein interaction motif. The 1.6-A crystal structure of the TRPV2-ARD, with six ankyrin repeats, reveals several atypical structural features. Repeats one through three display unusually long and flexible fingers with a large number of exposed aromatic residues, whereas repeats five and six have unusually long outer helices. Furthermore, a large counterclockwise twist observed in the stacking of repeats four and five breaks the regularity of the domain, altering the shape of surfaces available for interactions with proteins or other cellular ligands. Both solution studies and crystal packing interactions indicate that the TRPV2-ARD does not form homo-oligomers, suggesting that the ARD of TRPV ion channels may be used for interactions with regulatory factors rather than in promoting tetrameric assembly of the ion channels.
  Selected figure(s)  
Figure 1.
FIGURE 1. The TRPV2-ARD structure. A, primary structure of TRPV2. Ankyrin repeats are shown in labeled gray boxes; starred repeats are not recognized by sequence motif searches. B, left: Coomassie-stained gel of 2.5 µg of each of the three final protein samples used in crystallization, constructs 62-326, 75-321 (Se-Met substituted), and 75-321. Right: representative size exclusion chromatography trace of construct 75–321 on a Superdex 200 10/30 column. Arrows indicate elution volumes of molecular mass standards (molecular mass in kDa). C, ribbon diagram of TRPV2-ARD showing each ankyrin repeat in a distinct color. D, superposition of TRPV2-ARD structures. For clarity, only one chain from each crystal form is shown. Regions showing the most variability are colored green, gold, and blue for crystal forms I, II, and III, respectively. E, a large number of aromatic residues (shown in purple) are concentrated on the solvent-exposed surface of fingers 2 and 3.
Figure 2.
FIGURE 2. Structure-based sequence alignment of the six ankyrin repeats of TRPV2. A, a consensus ankyrin repeat sequence (16) is shown at the top, with designating a non-polar residue and x any residue. -Helices are red and 3[10] helices blue. Residues identical to consensus counterparts are boxed gray, showing a high level of conservation of a glycine at the second position and aliphatic residues in the inner and outer helices. The numbers in the last column are the lengths of inner/outer helices. B, superposition of repeats 1–4 of TRPV2-ARD (gold) and ankyrin (red, 1N11 (27); repeats 16–21 shown) highlights the large twist between repeats 4 and 5 of TRPV2-ARD.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 25006-25010) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20037586 G.Landouré, A.A.Zdebik, T.L.Martinez, B.G.Burnett, H.C.Stanescu, H.Inada, Y.Shi, A.A.Taye, L.Kong, C.H.Munns, S.S.Choo, C.B.Phelps, R.Paudel, H.Houlden, C.L.Ludlow, M.J.Caterina, R.Gaudet, R.Kleta, K.H.Fischbeck, and C.J.Sumner (2010).
Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.
  Nat Genet, 42, 170-174.
PDB codes: 3jxi 3jxj
20037587 H.X.Deng, C.J.Klein, J.Yan, Y.Shi, Y.Wu, F.Fecto, H.J.Yau, Y.Yang, H.Zhai, N.Siddique, E.T.Hedley-Whyte, R.Delong, M.Martina, P.J.Dyck, and T.Siddique (2010).
Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.
  Nat Genet, 42, 165-169.  
20926660 J.Mercado, A.Gordon-Shaag, W.N.Zagotta, and S.E.Gordon (2010).
Ca2+-dependent desensitization of TRPV2 channels is mediated by hydrolysis of phosphatidylinositol 4,5-bisphosphate.
  J Neurosci, 30, 13338-13347.  
21203922 W.Cheng, C.Sun, and J.Zheng (2010).
Heteromerization of TRP channel subunits: extending functional diversity.
  Protein Cell, 1, 802-810.  
19561608 H.Salazar, A.Jara-Oseguera, E.Hernández-García, I.Llorente, I.I.Arias-Olguín, M.Soriano-García, L.D.Islas, and T.Rosenbaum (2009).
Structural determinants of gating in the TRPV1 channel.
  Nat Struct Mol Biol, 16, 704-710.  
  19237587 R.Gaudet (2009).
Divide and conquer: high resolution structural information on TRP channel fragments.
  J Gen Physiol, 133, 231-237.  
20025796 R.Latorre, C.Zaelzer, and S.Brauchi (2009).
Structure-functional intimacies of transient receptor potential channels.
  Q Rev Biophys, 42, 201-246.  
  19237588 V.Y.Moiseenkova-Bell, and T.G.Wensel (2009).
Hot on the trail of TRP channel structure.
  J Gen Physiol, 133, 239-244.  
18232717 C.B.Phelps, R.J.Huang, P.V.Lishko, R.R.Wang, and R.Gaudet (2008).
Structural analyses of the ankyrin repeat domain of TRPV6 and related TRPV ion channels.
  Biochemistry, 47, 2476-2484.
PDB code: 2rfa
18297068 H.Salazar, I.Llorente, A.Jara-Oseguera, R.García-Villegas, M.Munari, S.E.Gordon, L.D.Islas, and T.Rosenbaum (2008).
A single N-terminal cysteine in TRPV1 determines activation by pungent compounds from onion and garlic.
  Nat Neurosci, 11, 255-261.  
18414734 R.Gaudet (2008).
A primer on ankyrin repeat function in TRP channels and beyond.
  Mol Biosyst, 4, 372-379.  
18490661 V.Y.Moiseenkova-Bell, L.A.Stanciu, I.I.Serysheva, B.J.Tobe, and T.G.Wensel (2008).
Structure of TRPV1 channel revealed by electron cryomicroscopy.
  Proc Natl Acad Sci U S A, 105, 7451-7455.  
17521566 D.L.Minor (2007).
The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data.
  Neuron, 54, 511-533.  
17706410 M.Bandell, L.J.Macpherson, and A.Patapoutian (2007).
From chills to chilis: mechanisms for thermosensation and chemesthesis via thermoTRPs.
  Curr Opin Neurobiol, 17, 490-497.  
17031667 T.Rohacs (2007).
Regulation of TRP channels by PIP(2).
  Pflugers Arch, 453, 753-762.  
  17325193 W.Cheng, F.Yang, C.L.Takanishi, and J.Zheng (2007).
Thermosensitive TRPV channel subunits coassemble into heteromeric channels with intermediate conductance and gating properties.
  J Gen Physiol, 129, 191-207.  
17018292 E.Procko, I.Ferrin-O'Connell, S.L.Ng, and R.Gaudet (2006).
Distinct structural and functional properties of the ATPase sites in an asymmetric ABC transporter.
  Mol Cell, 24, 51-62.
PDB codes: 2ixe 2ixf 2ixg
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.