PDBsum entry 3byh

Go to PDB code: 
protein Protein-protein interface(s) links
Structural protein PDB id
Jmol PyMol
Protein chains
374 a.a.
231 a.a. *
* Residue conservation analysis
PDB id:
Name: Structural protein
Title: Model of actin-fimbrin abd2 complex
Structure: Actin. Chain: a. Synonym: beta-actin, ps1tp5-binding protein 1. Engineered: yes. Fimbrin abd2. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ps1tp5bp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Authors: V.E.Galkin,A.Orlova,O.Cherepanova,M.C.Lebart,E.H.Egelman
Key ref:
V.E.Galkin et al. (2008). High-resolution cryo-EM structure of the F-actin-fimbrin/plastin ABD2 complex. Proc Natl Acad Sci U S A, 105, 1494-1498. PubMed id: 18234857 DOI: 10.1073/pnas.0708667105
16-Jan-08     Release date:   19-Feb-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P60709  (ACTB_HUMAN) -  Actin, cytoplasmic 1
375 a.a.
374 a.a.
Protein chain
No UniProt id for this chain
Struc: 231 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vesicle   19 terms 
  Biological process     Fc-gamma receptor signaling pathway involved in phagocytosis   13 terms 
  Biochemical function     nucleotide binding     12 terms  


DOI no: 10.1073/pnas.0708667105 Proc Natl Acad Sci U S A 105:1494-1498 (2008)
PubMed id: 18234857  
High-resolution cryo-EM structure of the F-actin-fimbrin/plastin ABD2 complex.
V.E.Galkin, A.Orlova, O.Cherepanova, M.C.Lebart, E.H.Egelman.
Many actin binding proteins have a modular architecture, and calponin-homology (CH) domains are one such structurally conserved module found in numerous proteins that interact with F-actin. The manner in which CH-domains bind F-actin has been controversial. Using cryo-EM and a single-particle approach to helical reconstruction, we have generated 12-A-resolution maps of F-actin alone and F-actin decorated with a fragment of human fimbrin (L-plastin) containing tandem CH-domains. The high resolution allows an unambiguous fit of the crystal structure of fimbrin into the map. The interaction between fimbrin ABD2 (actin binding domain 2) and F-actin is different from any interaction previously observed or proposed for tandem CH-domain proteins, showing that the structural conservation of the CH-domains does not lead to a conserved mode of interaction with F-actin. Both the stapling of adjacent actin protomers and the additional closure of the nucleotide binding cleft in F-actin when the fimbrin fragment binds may explain how fimbrin can stabilize actin filaments. A mechanism is proposed where ABD1 of fimbrin becomes activated for binding a second actin filament after ABD2 is bound to a first filament, and this can explain how mutations of residues buried in the interface between ABD2 and ABD1 can rescue temperature-sensitive defects in actin.
  Selected figure(s)  
Figure 2.
Three-dimensional reconstruction of ABD2–F-actin complex generated from a subset of segments (n = 8,357) chosen to eliminate heterogeneity. The volume has been filtered to 12-Å resolution and is shown with docked atomic models of actin and ABD2 (a). Actin subdomains are labeled with red numbers, and CH domains of ABD2 are labeled in black. Docking of actin was performed as described in Fig. 1, and CH3 and CH4 of ABD2 were docked independently. The atomic model of ABD2–F-actin complex is filtered to 12-Å resolution (b, blue mesh) and is superimposed on the actual map (b, transparent gray surface). Residues of actin shown to interact with fimbrin are shown as green spheres (c and d) and numbered in red (d), and residues of ABD2 important for interacting with F-actin are shown as yellow spheres (c and d) and numbered in black (d). The actin binding core of fimbrin in the conformation found in the crystal (22) is superimposed on the atomic model of actin filament derived from the ABD2–F-actin complex (d). CH-domains are marked as follows: CH1, magenta; CH2, cyan; CH3, red; CH4, orange.
Figure 3.
Perturbations of atomic models were needed to match the reconstruction. The ATP binding cleft of actin in the ABD2–F-actin complex is more closed (a, blue ribbon) than that in the pure F-actin reconstruction (a, green ribbon). This is due to an apparent rotation of subdomain 1 by ≈12° and a shift of subdomain 2 by ≈3.5 Å. To better fit CH4 into the reconstruction (b, green ribbon), it was rotated with respect to CH3 so that the most distal loop was shifted by 14 Å from its position in the crystal (b, red ribbon).
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20192778 B.Bugyi, and M.F.Carlier (2010).
Control of actin filament treadmilling in cell motility.
  Annu Rev Biophys, 39, 449-470.  
20025974 D.M.Paul, J.M.Squire, and E.P.Morris (2010).
A novel approach to the structural analysis of partially decorated actin based filaments.
  J Struct Biol, 170, 278-285.  
20368459 J.Pfaendtner, E.M.De La Cruz, and G.A.Voth (2010).
Actin filament remodeling by actin depolymerization factor/cofilin.
  Proc Natl Acad Sci U S A, 107, 7299-7304.  
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.  
20532239 M.Hertzog, F.Milanesi, L.Hazelwood, A.Disanza, H.Liu, E.Perlade, M.G.Malabarba, S.Pasqualato, A.Maiolica, S.Confalonieri, C.Le Clainche, N.Offenhauser, J.Block, K.Rottner, P.P.Di Fiore, M.F.Carlier, N.Volkmann, D.Hanein, and G.Scita (2010).
Molecular basis for the dual function of Eps8 on actin dynamics: bundling and capping.
  PLoS Biol, 8, e1000387.  
20844487 T.Fujii, A.H.Iwane, T.Yanagida, and K.Namba (2010).
Direct visualization of secondary structures of F-actin by electron cryomicroscopy.
  Nature, 467, 724-728.
PDB code: 3mfp
20637412 T.Oda, and Y.Maéda (2010).
Multiple Conformations of F-actin.
  Structure, 18, 761-767.  
20383143 V.E.Galkin, A.Orlova, A.Salmazo, K.Djinovic-Carugo, and E.H.Egelman (2010).
Opening of tandem calponin homology domains regulates their affinity for F-actin.
  Nat Struct Mol Biol, 17, 614-616.
PDB code: 3lue
20935633 V.E.Galkin, A.Orlova, G.F.Schröder, and E.H.Egelman (2010).
Structural polymorphism in F-actin.
  Nat Struct Mol Biol, 17, 1318-1323.  
20060835 V.E.Galkin, W.H.Schmied, O.Schraidt, T.C.Marlovits, and E.H.Egelman (2010).
The structure of the Salmonella typhimurium type III secretion system needle shows divergence from the flagellar system.
  J Mol Biol, 396, 1392-1397.  
20169155 Z.Al Tanoury, E.Schaffner-Reckinger, A.Halavatyi, C.Hoffmann, M.Moes, E.Hadzic, M.Catillon, M.Yatskou, and E.Friederich (2010).
Quantitative kinetic study of the actin-bundling protein L-plastin and of its impact on actin turn-over.
  PLoS One, 5, e9210.  
19504571 C.Thomas, S.Tholl, D.Moes, M.Dieterle, J.Papuga, F.Moreau, and A.Steinmetz (2009).
Actin bundling in plants.
  Cell Motil Cytoskeleton, 66, 940-957.  
19642111 E.H.Egelman, and L.A.Amos (2009).
Electron microscopy of helical filaments: rediscovering buried treasures in negative stain.
  Bioessays, 31, 909-911.  
19696342 H.Y.Kueh, and T.J.Mitchison (2009).
Structural plasticity in actin and tubulin polymer dynamics.
  Science, 325, 960-963.  
19767829 K.Pengelly, A.Loncar, A.A.Perieteanu, and J.F.Dawson (2009).
Cysteine engineering of actin self-assembly interfaces.
  Biochem Cell Biol, 87, 663-675.  
19748346 V.E.Galkin, A.Orlova, C.Rivera, R.D.Mullins, and E.H.Egelman (2009).
Structural polymorphism of the ParM filament and dynamic instability.
  Structure, 17, 1253-1264.
PDB codes: 3iku 3iky
19447181 V.H.Ramey, H.W.Wang, and E.Nogales (2009).
Ab initio reconstruction of helical samples with heterogeneity, disorder and coexisting symmetries.
  J Struct Biol, 167, 97.  
18952167 B.Sjöblom, J.Ylänne, and K.Djinović-Carugo (2008).
Novel structural insights into F-actin-binding and novel functions of calponin homology domains.
  Curr Opin Struct Biol, 18, 702-708.  
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.
  Structure, 16, 1882-1891.  
19436497 E.H.Egelman (2008).
Problems in fitting high resolution structures into electron microscopic reconstructions.
  HFSP J, 2, 324-331.  
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.