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PDBsum entry 1vii

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protein links
Actin binding PDB id
1vii
Jmol
Contents
Protein chain
36 a.a. *
* Residue conservation analysis
PDB id:
1vii
Name: Actin binding
Title: Thermostable subdomain from chicken villin headpiece, nmr, minimized average structure
Structure: Villin. Chain: a. Fragment: thermostable subdomain. Synonym: hp-36, r42-76. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: intestine. Tissue: epithelium. Cell: epithelial. Cellular_location: microvilli. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 1 models
Authors: C.J.Mcknight
Key ref: C.J.McKnight et al. (1997). NMR structure of the 35-residue villin headpiece subdomain. Nat Struct Biol, 4, 180-184. PubMed id: 9164455
Date:
15-Jan-97     Release date:   12-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02640  (VILI_CHICK) -  Villin-1
Seq:
Struc:
 
Seq:
Struc:
826 a.a.
36 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytoskeleton organization   1 term 
  Biochemical function     actin binding     1 term  

 

 
Nat Struct Biol 4:180-184 (1997)
PubMed id: 9164455  
 
 
NMR structure of the 35-residue villin headpiece subdomain.
C.J.McKnight, P.T.Matsudaira, P.S.Kim.
 
  ABSTRACT  
 
The NMR structure of an autonomously folding subdomain from villin headpiece is reported. It forms a novel three helix structure with the actin-binding residues arrayed on the C-terminal helix.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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21321226 J.K.Chung, M.C.Thielges, and M.D.Fayer (2011).
Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy.
  Proc Natl Acad Sci U S A, 108, 3578-3583.  
20197040 A.Kuzmanic, and B.Zagrovic (2010).
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.
  Biophys J, 98, 861-871.  
20194774 A.Reiner, P.Henklein, and T.Kiefhaber (2010).
An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain.
  Proc Natl Acad Sci U S A, 107, 4955-4960.  
19412905 I.H.Lee, S.Y.Kim, and J.Lee (2010).
Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure.
  J Comput Chem, 31, 57-65.  
20036210 J.M.Rogers, L.G.Lippert, and F.Gai (2010).
Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications.
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20000466 K.N.Hu, W.M.Yau, and R.Tycko (2010).
Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance.
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19647001 K.N.Hu, R.H.Havlin, W.M.Yau, and R.Tycko (2009).
Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance.
  J Mol Biol, 392, 1055-1073.  
19479944 L.Vugmeyster (2009).
Slow backbone dynamics of chicken villin headpiece subdomain probed by NMR C'-N cross-correlated relaxation.
  Magn Reson Chem, 47, 746-751.  
19618902 S.Bagchi, C.Falvo, S.Mukamel, and R.M.Hochstrasser (2009).
2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.
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19598233 W.Meng, B.Shan, Y.Tang, and D.P.Raleigh (2009).
Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein.
  Protein Sci, 18, 1692-1701.  
19081064 C.M.Hampton, J.Liu, D.W.Taylor, D.J.DeRosier, and K.A.Taylor (2008).
The 3D structure of villin as an unusual F-Actin crosslinker.
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18366016 D.Katagiri, H.Fuji, S.Neya, and T.Hoshino (2008).
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
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19045234 H.Lei, X.Deng, Z.Wang, and Y.Duan (2008).
The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier.
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18183310 J.Chen, and C.L.Brooks Iii (2008).
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
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19033473 J.Kubelka, E.R.Henry, T.Cellmer, J.Hofrichter, and W.A.Eaton (2008).
Chemical, physical, and theoretical kinetics of an ultrafast folding protein.
  Proc Natl Acad Sci U S A, 105, 18655-18662.  
18820237 L.Vugmeyster, and C.J.McKnight (2008).
Slow motions in chicken villin headpiece subdomain probed by cross-correlated NMR relaxation of amide NH bonds in successive residues.
  Biophys J, 95, 5941-5950.  
18312148 R.Anandakrishnan, and A.Onufriev (2008).
Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules.
  J Comput Biol, 15, 165-184.  
18284690 W.Gronwald, T.Hohm, and D.Hoffmann (2008).
Evolutionary Pareto-optimization of stably folding peptides.
  BMC Bioinformatics, 9, 109.
PDB code: 2ppz
18205480 Y.Wei, W.Nadler, and U.H.Hansmann (2008).
Backbone and side-chain ordering in a small protein.
  J Chem Phys, 128, 025105.  
17563390 D.Lucent, V.Vishal, and V.S.Pande (2007).
Protein folding under confinement: a role for solvent.
  Proc Natl Acad Sci U S A, 104, 10430-10434.  
17123960 G.Cornilescu, E.B.Hadley, M.G.Woll, J.L.Markley, S.H.Gellman, and C.C.Cornilescu (2007).
Solution structure of a small protein containing a fluorinated side chain in the core.
  Protein Sci, 16, 14-19.
PDB code: 2jm0
17098444 G.Jayachandran, V.Vishal, A.E.García, and V.S.Pande (2007).
Local structure formation in simulations of two small proteins.
  J Struct Biol, 157, 491-499.  
17360390 H.Lei, C.Wu, H.Liu, and Y.Duan (2007).
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.
  Proc Natl Acad Sci U S A, 104, 4925-4930.  
17512537 H.Lei, and Y.Duan (2007).
Two-stage folding of HP-35 from ab initio simulations.
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17279501 H.Yuki, Y.Tanaka, M.Hata, H.Ishikawa, S.Neya, and T.Hoshino (2007).
Implementation of pi-pi interactions in molecular dynamics simulation.
  J Comput Chem, 28, 1091-1099.  
17411115 M.J.Schnieders, N.A.Baker, P.Ren, and J.W.Ponder (2007).
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
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18185008 S.Senturk, S.Baday, Y.Arkun, and B.Erman (2007).
Optimum folding pathways for growing protein chains.
  Phys Biol, 4, 305-316.  
16425239 B.Zagrovic, and W.F.van Gunsteren (2006).
Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
  Proteins, 63, 210-218.  
16674165 G.Jayachandran, V.Vishal, and V.S.Pande (2006).
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece.
  J Chem Phys, 124, 164902.  
16965062 S.Bandyopadhyay, S.Chakraborty, and B.Bagchi (2006).
Coupling between hydration layer dynamics and unfolding kinetics of HP-36.
  J Chem Phys, 125, 084912.  
16963648 S.Jang, N.Sreerama, V.H.Liao, S.H.Lu, F.Y.Li, S.Shin, R.W.Woody, and S.H.Lin (2006).
Theoretical investigation of the photoinitiated folding of HP-36.
  Protein Sci, 15, 2290-2299.  
17098192 S.Rauscher, S.Baud, M.Miao, F.W.Keeley, and R.Pomès (2006).
Proline and glycine control protein self-organization into elastomeric or amyloid fibrils.
  Structure, 14, 1667-1676.  
15533926 F.Ding, S.V.Buldyrev, and N.V.Dokholyan (2005).
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
  Biophys J, 88, 147-155.  
15521059 G.M.De Mori, G.Colombo, and C.Micheletti (2005).
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.
  Proteins, 58, 459-471.  
16392943 J.M.Carr, and D.J.Wales (2005).
Global optimization and folding pathways of selected alpha-helical proteins.
  J Chem Phys, 123, 234901.  
16008483 J.M.Carr, S.A.Trygubenko, and D.J.Wales (2005).
Finding pathways between distant local minima.
  J Chem Phys, 122, 234903.  
15754302 M.Y.Shen, and K.F.Freed (2005).
A simple method for faster nonbonded force evaluations.
  J Comput Chem, 26, 691-698.  
15718283 R.H.Havlin, and R.Tycko (2005).
Probing site-specific conformational distributions in protein folding with solid-state NMR.
  Proc Natl Acad Sci U S A, 102, 3284-3289.  
16269546 S.H.Brewer, D.M.Vu, Y.Tang, Y.Li, S.Franzen, D.P.Raleigh, and R.B.Dyer (2005).
Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain.
  Proc Natl Acad Sci U S A, 102, 16662-16667.  
15894611 T.K.Chiu, J.Kubelka, R.Herbst-Irmer, W.A.Eaton, J.Hofrichter, and D.R.Davies (2005).
High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein.
  Proc Natl Acad Sci U S A, 102, 7517-7522.
PDB codes: 1wy3 1wy4 1yrf 1yri
14660664 B.S.Frank, D.Vardar, A.H.Chishti, and C.J.McKnight (2004).
The NMR structure of dematin headpiece reveals a dynamic loop that is conformationally altered upon phosphorylation at a distal site.
  J Biol Chem, 279, 7909-7916.
PDB code: 1qzp
15454426 B.Zagrovic, and V.S.Pande (2004).
How does averaging affect protein structure comparison on the ensemble level?
  Biophys J, 87, 2240-2246.  
15096633 W.Vermeulen, P.Vanhaesebrouck, M.Van Troys, M.Verschueren, F.Fant, M.Goethals, C.Ampe, J.C.Martins, and F.A.Borremans (2004).
Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements.
  Protein Sci, 13, 1276-1287.
PDB codes: 1unc 1und
12857859 A.Gloss, F.Rivero, N.Khaire, R.Müller, W.F.Loomis, M.Schleicher, and A.A.Noegel (2003).
Villidin, a novel WD-repeat and villin-related protein from Dictyostelium, is associated with membranes and the cytoskeleton.
  Mol Biol Cell, 14, 2716-2727.  
14555998 B.Zagrovic, and V.S.Pande (2003).
Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.
  Nat Struct Biol, 10, 955-961.  
12827676 M.S.Lee, M.Feig, F.R.Salsbury, and C.L.Brooks (2003).
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.
  J Comput Chem, 24, 1348-1356.  
12517699 S.J.Winder (2003).
Structural insights into actin-binding, branching and bundling proteins.
  Curr Opin Cell Biol, 15, 14-22.  
12606551 S.Rossenu, S.Leyman, D.Dewitte, D.Peelaers, V.Jonckheere, M.Van Troys, J.Vandekerckhove, and C.Ampe (2003).
A phage display-based method for determination of relative affinities of mutants. Application of the actin-binding motifs in thymosin beta 4 and the villin headpiece.
  J Biol Chem, 278, 16642-16650.  
12579582 V.S.Pande, I.Baker, J.Chapman, S.P.Elmer, S.Khaliq, S.M.Larson, Y.M.Rhee, M.R.Shirts, C.D.Snow, E.J.Sorin, and B.Zagrovic (2003).
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.
  Biopolymers, 68, 91.  
11847290 B.S.Frank, D.Vardar, D.A.Buckley, and C.J.McKnight (2002).
The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain.
  Protein Sci, 11, 680-687.  
12032551 S.H.Gellman, and D.N.Woolfson (2002).
Mini-proteins Trp the light fantastic.
  Nat Struct Biol, 9, 408-410.  
11746709 Y.Liu, and D.L.Beveridge (2002).
Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
  Proteins, 46, 128-146.  
11583620 C.H.Lin, B.J.Hare, G.Wagner, S.C.Harrison, T.Maniatis, and E.Fraenkel (2001).
A small domain of CBP/p300 binds diverse proteins: solution structure and functional studies.
  Mol Cell, 8, 581-590.
PDB code: 1jjs
11435115 C.Laguri, B.Gilquin, N.Wolff, R.Romi-Lebrun, K.Courchay, I.Callebaut, H.J.Worman, and S.Zinn-Justin (2001).
Structural characterization of the LEM motif common to three human inner nuclear membrane proteins.
  Structure, 9, 503-511.
PDB codes: 1h9e 1h9f
10848969 C.Simenel, M.Van Troys, J.Vandekerckhove, C.Ampe, and M.Delepierre (2000).
Structural requirements for thymosin beta4 in its contact with actin. An NMR-analysis of thymosin beta4 mutants in solution and correlation with their biological activity.
  Eur J Biochem, 267, 3530-3538.  
10671519 F.Lin, D.L.Blake, I.Callebaut, I.S.Skerjanc, L.Holmer, M.W.McBurney, M.Paulin-Levasseur, and H.J.Worman (2000).
MAN1, an inner nuclear membrane protein that shares the LEM domain with lamina-associated polypeptide 2 and emerin.
  J Biol Chem, 275, 4840-4847.  
10991195 P.Derreumaux (2000).
Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations.
  Phys Rev Lett, 85, 206-209.  
  10595528 A.K.Chamberlain, K.F.Fischer, D.Reardon, T.M.Handel, and A.S.Marqusee (1999).
Folding of an isolated ribonuclease H core fragment.
  Protein Sci, 8, 2251-2257.  
10517154 B.Imperiali, and J.J.Ottesen (1999).
Uniquely folded mini-protein motifs.
  J Pept Res, 54, 177-184.  
  10074138 B.Liu, R.Dai, C.J.Tian, L.Dawson, R.Gorelick, and X.F.Yu (1999).
Interaction of the human immunodeficiency virus type 1 nucleocapsid with actin.
  J Virol, 73, 2901-2908.  
10480879 E.Friederich, K.Vancompernolle, D.Louvard, and J.Vandekerckhove (1999).
Villin function in the organization of the actin cytoskeleton. Correlation of in vivo effects to its biochemical activities in vitro.
  J Biol Chem, 274, 26751-26760.  
  10386879 L.Wang, Y.Duan, R.Shortle, B.Imperiali, and P.A.Kollman (1999).
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures.
  Protein Sci, 8, 1292-1304.  
9990286 M.Van Troys, J.Vandekerckhove, and C.Ampe (1999).
Structural modules in actin-binding proteins: towards a new classification.
  Biochim Biophys Acta, 1448, 323-348.  
9888821 R.W.Lim, R.Furukawa, S.Eagle, R.C.Cartwright, and M.Fechheimer (1999).
Three distinct F-actin binding sites in the Dictyostelium discoideum 34,000 dalton actin bundling protein.
  Biochemistry, 38, 800-812.  
10194328 S.Spector, P.Young, and D.P.Raleigh (1999).
Nativelike structure and stability in a truncation mutant of a protein minidomain: the peripheral subunit-binding domain.
  Biochemistry, 38, 4128-4136.  
9631289 A.McGough (1998).
F-actin-binding proteins.
  Curr Opin Struct Biol, 8, 166-176.  
9763424 J.R.Bartles, L.Zheng, A.Li, A.Wierda, and B.Chen (1998).
Small espin: a third actin-bundling protein and potential forked protein ortholog in brush border microvilli.
  J Cell Biol, 143, 107-119.  
9565754 M.Struthers, J.J.Ottesen, and B.Imperiali (1998).
Design and NMR analyses of compact, independently folded BBA motifs.
  Fold Des, 3, 95.
PDB code: 1t8j
9748471 O.Turunen, M.Sainio, J.Jääskeläinen, O.Carpén, and A.Vaheri (1998).
Structure-function relationships in the ezrin family and the effect of tumor-associated point mutations in neurofibromatosis 2 protein.
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9585532 P.O.Freskgârd, L.C.Petersen, D.A.Gabriel, X.Li, and E.Persson (1998).
Conformational stability of factor VIIa: biophysical studies of thermal and guanidine hydrochloride-induced denaturation.
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9484592 Y.A.Puius, N.M.Mahoney, and S.C.Almo (1998).
The modular structure of actin-regulatory proteins.
  Curr Opin Cell Biol, 10, 23-34.  
9707572 Y.Duan, L.Wang, and P.A.Kollman (1998).
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation.
  Proc Natl Acad Sci U S A, 95, 9897-9902.  
9784131 Y.Duan, and P.A.Kollman (1998).
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
  Science, 282, 740-744.  
9311930 B.I.Dahiyat, and S.L.Mayo (1997).
De novo protein design: fully automated sequence selection.
  Science, 278, 82-87.
PDB codes: 1fsd 1fsm 1fsv
9382871 K.N.Pestonjamasp, R.K.Pope, J.D.Wulfkuhle, and E.J.Luna (1997).
Supervillin (p205): A novel membrane-associated, F-actin-binding protein in the villin/gelsolin superfamily.
  J Cell Biol, 139, 1255-1269.  
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.