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PDBsum entry 3hte

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protein ligands Protein-protein interface(s) links
Motor protein PDB id
3hte
Jmol
Contents
Protein chains
317 a.a. *
283 a.a. *
301 a.a. *
Ligands
SO4 ×6
* Residue conservation analysis
PDB id:
3hte
Name: Motor protein
Title: Crystal structure of nucleotide-free hexameric clpx
Structure: Atp-dependent clp protease atp-binding subunit cl chain: a, b, c, d, e, f. Fragment: covalently linked clpx residues 62-424. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b0438, clpx, jw0428, lopc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
4.03Å     R-factor:   0.279     R-free:   0.313
Authors: S.E.Glynn,A.Martin,T.A.Baker,R.T.Sauer
Key ref: S.E.Glynn et al. (2009). Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell, 139, 744-756. PubMed id: 19914167
Date:
11-Jun-09     Release date:   24-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6H1  (CLPX_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpX
Seq:
Struc:
424 a.a.
317 a.a.*
Protein chain
Pfam   ArchSchema ?
P0A6H1  (CLPX_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpX
Seq:
Struc:
424 a.a.
283 a.a.*
Protein chains
Pfam   ArchSchema ?
P0A6H1  (CLPX_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpX
Seq:
Struc:
424 a.a.
301 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein folding   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
Cell 139:744-756 (2009)
PubMed id: 19914167  
 
 
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, R.T.Sauer.
 
  ABSTRACT  
 
ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22237024 G.C.Lander, E.Estrin, M.E.Matyskiela, C.Bashore, E.Nogales, and A.Martin (2012).
Complete subunit architecture of the proteasome regulatory particle.
  Nature, 482, 186-191.  
22426545 H.Schmidt, E.S.Gleave, and A.P.Carter (2012).
Insights into dynein motor domain function from a 3.3-Å crystal structure.
  Nat Struct Mol Biol, 19, 492.
PDB codes: 4ai6 4akg 4akh 4aki
22562135 S.E.Glynn, A.R.Nager, T.A.Baker, and R.T.Sauer (2012).
Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine.
  Nat Struct Mol Biol, 19, 616-622.  
22020261 E.Gur, D.Biran, and E.Z.Ron (2011).
Regulated proteolysis in Gram-negative bacteria--how and when?
  Nat Rev Microbiol, 9, 839-848.  
21368759 F.Wang, Z.Mei, Y.Qi, C.Yan, Q.Hu, J.Wang, and Y.Shi (2011).
Structure and mechanism of the hexameric MecA-ClpC molecular machine.
  Nature, 471, 331-335.
PDB codes: 2y1q 2y1r 3pxg 3pxi
22037170 G.Tian, S.Park, M.J.Lee, B.Huck, F.McAllister, C.P.Hill, S.P.Gygi, and D.Finley (2011).
An asymmetric interface between the regulatory and core particles of the proteasome.
  Nat Struct Mol Biol, 18, 1259-1267.  
22056769 M.Stotz, O.Mueller-Cajar, S.Ciniawsky, P.Wendler, F.U.Hartl, A.Bracher, and M.Hayer-Hartl (2011).
Structure of green-type Rubisco activase from tobacco.
  Nat Struct Mol Biol, 18, 1366-1370.
PDB codes: 3t15 3zw6
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
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.