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PDBsum entry 1u4q

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protein Protein-protein interface(s) links
Structural protein PDB id
1u4q
Jmol
Contents
Protein chains
318 a.a. *
Waters ×445
* Residue conservation analysis
PDB id:
1u4q
Name: Structural protein
Title: Crystal structure of repeats 15, 16 and 17 of chicken brain alpha spectrin
Structure: Spectrin alpha chain, brain. Chain: a, b. Fragment: repeats 15, 16, 17 (residues 1662 to 1982). Synonym: alpha spectrin, spectrin, non-erythroid alpha chain, fodrin alpha chain. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: brain. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.223     R-free:   0.313
Authors: H.Kusunoki,G.Minasov,R.I.Macdonald,A.Mondragon
Key ref:
H.Kusunoki et al. (2004). Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin. J Mol Biol, 344, 495-511. PubMed id: 15522301 DOI: 10.1016/j.jmb.2004.09.019
Date:
26-Jul-04     Release date:   19-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07751  (SPTA2_CHICK) -  Spectrin alpha chain, non-erythrocytic 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2477 a.a.
318 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.jmb.2004.09.019 J Mol Biol 344:495-511 (2004)
PubMed id: 15522301  
 
 
Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin.
H.Kusunoki, G.Minasov, R.I.Macdonald, A.Mondragón.
 
  ABSTRACT  
 
Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain alpha-spectrin and human erythroid beta-spectrin repeats can undergo bending without losing their alpha-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain alpha-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, the three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of alpha-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and alpha-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Electron density maps of linker regions of CBa15-17. Stereo views of the final 2F[o] -F[c] maps around the linker region between R15 and R16 (top panel) and between R16 and R17 (bottom panel) at 2.5 Å resolution. The maps are contoured at the 1.0 s level and shown by a blue mesh. The final models of the linker regions are shown with a color scheme identical with that in Figure 2.
Figure 4.
Figure 4. CBa15-17 dimer. A, Ribbon diagrams of the CBa15-17 dimer (left panel) and a-actinin dimer (right panel) are shown. In CBa15-17, R15 (residues 1665-1770) is shown in orange, R16 (residues 1771-1876) in yellow, and R17 (residues 1877-1981) in green. Residues 1662-1664 in molecule A are shown in white. In a-actinin, R1 (residues 274-393) is shown in white, R2 (residues 394-508) in pink, R3 (residues 509-633) in magenta, and R4 (residues 634-746) in blue. Residues 272 and 273 are shown in brown. B, Space-filling models of the CBa15-17 dimer (left panel) and a-actinin dimer (right panel) are shown. The color scheme is identical with that in A. The lines were drawn to delineate the boundaries of repeat pairs.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 495-511) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20411297 A.Czogalla, and A.F.Sikorski (2010).
Do we already know how spectrin attracts ankyrin?
  Cell Mol Life Sci, 67, 2679-2683.  
  19959814 A.Lin, A.Hokugo, J.Choi, and I.Nishimura (2010).
Small cytoskeleton-associated molecule, fibroblast growth factor receptor 1 oncogene partner 2/wound inducible transcript-3.0 (FGFR1OP2/wit3.0), facilitates fibroblast-driven wound closure.
  Am J Pathol, 176, 108-121.  
20130652 B.G.Wensley, S.Batey, F.A.Bone, Z.M.Chan, N.R.Tumelty, A.Steward, L.G.Kwa, A.Borgia, and J.Clarke (2010).
Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family.
  Nature, 463, 685-688.  
20493457 H.Saitsu, J.Tohyama, T.Kumada, K.Egawa, K.Hamada, I.Okada, T.Mizuguchi, H.Osaka, R.Miyata, T.Furukawa, K.Haginoya, H.Hoshino, T.Goto, Y.Hachiya, T.Yamagata, S.Saitoh, T.Nagai, K.Nishiyama, A.Nishimura, N.Miyake, M.Komada, K.Hayashi, S.Hirai, K.Ogata, M.Kato, A.Fukuda, and N.Matsumoto (2010).
Dominant-negative mutations in alpha-II spectrin cause West syndrome with severe cerebral hypomyelination, spastic quadriplegia, and developmental delay.
  Am J Hum Genet, 86, 881-891.  
20197550 J.J.Ipsaro, S.L.Harper, T.E.Messick, R.Marmorstein, A.Mondragón, and D.W.Speicher (2010).
Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex.
  Blood, 115, 4843-4852.
PDB code: 3lbx
20195380 J.W.Brown, and C.J.McKnight (2010).
Molecular model of the microvillar cytoskeleton and organization of the brush border.
  PLoS One, 5, e9406.  
  19847780 P.Eastman, and V.S.Pande (2010).
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.
  J Comput Chem, 31, 1268-1272.  
20563238 Z.Zhong, S.A.Chang, A.Kalinowski, K.L.Wilson, and K.N.Dahl (2010).
Stabilization of the spectrin-like domains of nesprin-1alpha by the evolutionarily conserved "adaptive" domain.
  Cell Mol Bioeng, 3, 139-150.  
19445951 B.G.Wensley, M.Gärtner, W.X.Choo, S.Batey, and J.Clarke (2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
  J Mol Biol, 390, 1074-1085.  
19436721 J.Golji, R.Collins, and M.R.Mofrad (2009).
Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior.
  PLoS Comput Biol, 5, e1000389.  
19141864 J.J.Ipsaro, L.Huang, and A.Mondragón (2009).
Structures of the spectrin-ankyrin interaction binding domains.
  Blood, 113, 5385-5393.
PDB codes: 3f57 3f59
19098307 L.Davis, K.Abdi, M.Machius, C.Brautigam, D.R.Tomchick, V.Bennett, and P.Michaely (2009).
Localization and Structure of the Ankyrin-binding Site on {beta}2-Spectrin.
  J Biol Chem, 284, 6982-6987.
PDB code: 3edv
19191337 M.S.Friedrichs, P.Eastman, V.Vaidyanathan, M.Houston, S.Legrand, A.L.Beberg, D.L.Ensign, C.M.Bruns, and V.S.Pande (2009).
Accelerating molecular dynamic simulation on graphics processing units.
  J Comput Chem, 30, 864-872.  
19168783 P.R.Stabach, I.Simonović, M.A.Ranieri, M.S.Aboodi, T.A.Steitz, M.Simonovi, and J.S.Morrow (2009).
The structure of the ankyrin-binding site of beta-spectrin reveals how tandem spectrin-repeats generate unique ligand-binding properties.
  Blood, 113, 5377-5384.
PDB code: 3edu
20031633 R.W.Kaspar, H.D.Allen, W.C.Ray, C.E.Alvarez, J.T.Kissel, A.Pestronk, R.B.Weiss, K.M.Flanigan, J.R.Mendell, and F.Montanaro (2009).
Analysis of dystrophin deletion mutations predicts age of cardiomyopathy onset in becker muscular dystrophy.
  Circ Cardiovasc Genet, 2, 544-551.  
19158079 S.Legardinier, B.Legrand, C.Raguénès-Nicol, A.Bondon, S.Hardy, C.Tascon, E.Le Rumeur, and J.F.Hubert (2009).
A Two-amino Acid Mutation Encountered in Duchenne Muscular Dystrophy Decreases Stability of the Rod Domain 23 (R23) Spectrin-like Repeat of Dystrophin.
  J Biol Chem, 284, 8822-8832.  
17977835 D.Li, H.Y.Tang, and D.W.Speicher (2008).
A structural model of the erythrocyte spectrin heterodimer initiation site determined using homology modeling and chemical cross-linking.
  J Biol Chem, 283, 1553-1562.  
18223005 E.Eyal, and I.Bahar (2008).
Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models.
  Biophys J, 94, 3424-3435.  
19436439 S.Batey, A.A.Nickson, and J.Clarke (2008).
Studying the folding of multidomain proteins.
  HFSP J, 2, 365-377.  
18371978 S.Batey, and J.Clarke (2008).
The folding pathway of a single domain in a multidomain protein is not affected by its neighbouring domain.
  J Mol Biol, 378, 297-301.  
17192394 C.P.Johnson, M.Gaetani, V.Ortiz, N.Bhasin, S.Harper, P.G.Gallagher, D.W.Speicher, and D.E.Discher (2007).
Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding.
  Blood, 109, 3538-3543.  
17085494 L.G.Randles, R.W.Rounsevell, and J.Clarke (2007).
Spectrin domains lose cooperativity in forced unfolding.
  Biophys J, 92, 571-577.  
17867784 S.Paramore, G.S.Ayton, and G.A.Voth (2007).
Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem.
  J Chem Phys, 127, 105105.  
17029004 A.Chakrabarti, D.A.Kelkar, and A.Chattopadhyay (2006).
Spectrin organization and dynamics: new insights.
  Biosci Rep, 26, 369-386.  
17108086 S.Batey, and J.Clarke (2006).
Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains.
  Proc Natl Acad Sci U S A, 103, 18113-18118.  
16891371 S.Paramore, and G.A.Voth (2006).
Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules.
  Biophys J, 91, 3436-3445.  
16227506 S.Paramore, G.S.Ayton, D.T.Mirijanian, and G.A.Voth (2006).
Extending a spectrin repeat unit. I: linear force-extension response.
  Biophys J, 90, 92.  
16227505 S.Paramore, G.S.Ayton, and G.A.Voth (2006).
Extending a spectrin repeat unit. II: rupture behavior.
  Biophys J, 90, 101-111.  
16476728 X.An, X.Guo, X.Zhang, A.J.Baines, G.Debnath, D.Moyo, M.Salomao, N.Bhasin, C.Johnson, D.Discher, W.B.Gratzer, and N.Mohandas (2006).
Conformational stabilities of the structural repeats of erythroid spectrin and their functional implications.
  J Biol Chem, 281, 10527-10532.  
16230614 A.J.Wilcox, J.Choy, C.Bustamante, and A.Matouschek (2005).
Effect of protein structure on mitochondrial import.
  Proc Natl Acad Sci U S A, 102, 15435-15440.  
15988023 P.R.Bois, R.A.Borgon, C.Vonrhein, and T.Izard (2005).
Structural dynamics of alpha-actinin-vinculin interactions.
  Mol Cell Biol, 25, 6112-6122.
PDB code: 1ydi
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.