PDBsum entry 3hyb

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Chaperone PDB id
Protein chains
115 a.a. *
Waters ×44
* Residue conservation analysis
PDB id:
Name: Chaperone
Title: Crystal structure of rbcx from anabaena, crystal form ii
Structure: Rbcx protein. Chain: a, b. Engineered: yes
Source: Anabaena sp.. Organism_taxid: 1167. Gene: rbcx. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.30Å     R-factor:   0.247     R-free:   0.275
Authors: A.Bracher,C.Liu
Key ref:
C.Liu et al. (2010). Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Nature, 463, 197-202. PubMed id: 20075914 DOI: 10.1038/nature08651
22-Jun-09     Release date:   19-Jan-10    
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Protein chains
Pfam   ArchSchema ?
Q44212  (Q44212_9NOST) -  RbcX protein
135 a.a.
115 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1038/nature08651 Nature 463:197-202 (2010)
PubMed id: 20075914  
Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
C.Liu, A.L.Young, A.Starling-Windhof, A.Bracher, S.Saschenbrecker, B.V.Rao, K.V.Rao, O.Berninghausen, T.Mielke, F.U.Hartl, R.Beckmann, M.Hayer-Hartl.
Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.
  Selected figure(s)  
Figure 4.
Figure 4: RbcX[2]–RbcL interactions. a, Close-up of a top view of RbcL[8]–(RbcX[2])[8] (yellow mesh) showing the RbcL C terminus (red, residues 413–475) interacting with RbcX[2] (gold) (dashed box Fig. 3g). The RbcL C terminus is shown with the conserved residues F467 and F469 inserting into the hydrophobic binding pockets of RbcX[2]. b, Close-up of a side view of RbcL[8]–(RbcX[2])[8] with RbcX[2] interacting with the N-terminal domain of an adjacent RbcL (dashed box Fig. 3h). Conserved RbcX[2] residues Q29, E32, T33 and N34 are shown as blue spheres; candidate regions on RbcL for interaction with RbcX[2] are in pink. The C-terminal sequence of the adjacent RbcL reaching into the groove of RbcX[2] is seen in the background (red). c, Crosslinking of Syn6301-RbcL[8]–AnaCA-(RbcX[2])[8] complex. Isolated complex with RbcX[2] containing pBpa at the positions indicated was exposed to ultraviolet light (UV) and analysed together with non-exposed controls by anti-RbcL immunoblotting. Photoadducts are indicated by open arrowheads. Control, RbcL[8]–(RbcX[2])[8] complex without crosslinker. In the ribbon diagram of form II AnaCA-RbcX[2], amino-acid positions (labelled in one chain) that resulted in crosslinking are shown in blue and non-reactive positions in red.
Figure 6.
Figure 6: Model of GroEL/ES and RbcX[2]-assisted folding and assembly of Rubisco. a, Folded RbcL with a disordered C-terminal region is transiently released from the GroEL/GroES. b, RbcX[2] binds to the exposed RbcL C terminus, c, RbcL dimers are formed, ‘stapled’ together by the interaction of RbcX[2] with the C terminus of one RbcL and the N-terminal domain of the adjacent subunit. d, Stable dimers assemble to RbcL[8]–(RbcX[2])[8] complexes. e, RbcS binding weakens the RbcL–RbcX[2] interaction. Dissociation of RbcX[2] and binding of RbcS may occur in a stepwise manner, populating intermediates. f, RbcX[2] dissociates, enabling the C-terminal region of RbcL to adopt its final position and allowing maturation of Rubisco.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2010, 463, 197-202) copyright 2010.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22334143 L.Davis, and J.W.Chin (2012).
Designer proteins: applications of genetic code expansion in cell biology.
  Nat Rev Mol Cell Biol, 13, 168-182.  
21765418 A.Bracher, A.Starling-Windhof, F.U.Hartl, and M.Hayer-Hartl (2011).
Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco.
  Nat Struct Mol Biol, 18, 875-880.
PDB code: 3rg6
21776078 F.U.Hartl, A.Bracher, and M.Hayer-Hartl (2011).
Molecular chaperones in protein folding and proteostasis.
  Nature, 475, 324-332.  
21030385 M.A.Parry, M.Reynolds, M.E.Salvucci, C.Raines, P.J.Andralojc, X.G.Zhu, G.D.Price, A.G.Condon, and R.T.Furbank (2011).
Raising yield potential of wheat. II. Increasing photosynthetic capacity and efficiency.
  J Exp Bot, 62, 453-467.  
22048315 O.Mueller-Cajar, M.Stotz, P.Wendler, F.U.Hartl, A.Bracher, and M.Hayer-Hartl (2011).
Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
  Nature, 479, 194-199.
PDB codes: 3syk 3syl 3zuh
21166808 S.A.Goff (2011).
A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding.
  New Phytol, 189, 923-937.  
20727772 A.Chari, and U.Fischer (2010).
Cellular strategies for the assembly of molecular machines.
  Trends Biochem Sci, 35, 676-683.  
20075906 R.J.Ellis (2010).
Biochemistry: Tackling unintelligent design.
  Nature, 463, 164-165.  
20498370 S.Falk, and I.Sinning (2010).
cpSRP43 is a novel chaperone specific for light-harvesting chlorophyll a,b-binding proteins.
  J Biol Chem, 285, 21655-21661.  
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.