PDBsum entry 3hu3

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protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
Jmol PyMol
Protein chains
453 a.a. *
AGS ×2
_MG ×2
Waters ×263
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Structure of p97 n-d1 r155h mutant in complex with atpgs
Structure: Transitional endoplasmic reticulum atpase. Chain: a, b. Fragment: residues 1-481. Synonym: ter atpase, 15s mg(2+)-atpase p97 subunit, valosin containing protein, vcp. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: human. Gene: p97, vcp. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.172     R-free:   0.193
Authors: W.-K.Tang
Key ref: W.K.Tang et al. (2010). A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants. EMBO J, 29, 2217-2229. PubMed id: 20512113
12-Jun-09     Release date:   16-Jun-10    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P55072  (TERA_HUMAN) -  Transitional endoplasmic reticulum ATPase
806 a.a.
453 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
Bound ligand (Het Group name = AGS)
matches with 93.75% similarity
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     ATP binding     1 term  


EMBO J 29:2217-2229 (2010)
PubMed id: 20512113  
A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants.
W.K.Tang, D.Li, C.C.Li, L.Esser, R.Dai, L.Guo, D.Xia.
Mutations in p97, a major cytosolic AAA (ATPases associated with a variety of cellular activities) chaperone, cause inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD). IBMPFD mutants have single amino-acid substitutions at the interface between the N-terminal domain (N-domain) and the adjacent AAA domain (D1), resulting in a reduced affinity for ADP. The structures of p97 N-D1 fragments bearing IBMPFD mutations adopt an atypical N-domain conformation in the presence of Mg(2+).ATPgammaS, which is reversible by ADP, showing for the first time the nucleotide-dependent conformational change of the N-domain. The transition from the ADP- to the ATPgammaS-bound state is accompanied by a loop-to-helix conversion in the N-D1 linker and by an apparent re-ordering in the N-terminal region of p97. X-ray scattering experiments suggest that wild-type p97 subunits undergo a similar nucleotide-dependent N-domain conformational change. We propose that IBMPFD mutations alter the timing of the transition between nucleotide states by destabilizing the ADP-bound form and consequently interfere with the interactions between the N-domains and their substrates.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22298039 H.Meyer, M.Bug, and S.Bremer (2012).
Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system.
  Nat Cell Biol, 14, 117-123.  
22307055 L.F.Chang, S.Chen, C.C.Liu, X.Pan, J.Jiang, X.C.Bai, X.Xie, H.W.Wang, and S.F.Sui (2012).
Structural characterization of full-length NSF and 20S particles.
  Nat Struct Mol Biol, 19, 268-275.  
21152665 E.Chapman, A.N.Fry, and M.Kang (2011).
The complexities of p97 function in health and disease.
  Mol Biosyst, 7, 700-710.  
21145000 J.O.Johnson, J.Mandrioli, M.Benatar, Y.Abramzon, V.M.Van Deerlin, J.Q.Trojanowski, J.R.Gibbs, M.Brunetti, S.Gronka, J.Wuu, J.Ding, L.McCluskey, M.Martinez-Lage, D.Falcone, D.G.Hernandez, S.Arepalli, S.Chong, J.C.Schymick, J.Rothstein, F.Landi, Y.D.Wang, A.Calvo, G.Mora, M.Sabatelli, M.R.Monsurrò, S.Battistini, F.Salvi, R.Spataro, P.Sola, G.Borghero, G.Galassi, S.W.Scholz, J.P.Taylor, G.Restagno, A.Chiò, B.J.Traynor, F.Giannini, C.Ricci, C.Moglia, I.Ossola, A.Canosa, S.Gallo, G.Tedeschi, P.Sola, I.Bartolomei, K.Marinou, L.Papetti, A.Conte, M.Luigetti, V.La Bella, P.Paladino, C.Caponnetto, P.Volanti, M.G.Marrosu, and M.R.Murru (2010).
Exome sequencing reveals VCP mutations as a cause of familial ALS.
  Neuron, 68, 857-864.  
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.