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PDBsum entry 1qcs
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Fusion protein PDB id
1qcs

 

 

 

 

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Contents
Protein chain
195 a.a. *
Ligands
SO4 ×3
Waters ×130
* Residue conservation analysis
PDB id:
1qcs
Name: Fusion protein
Title: N-terminal domain of n-ethylmaleimide sensitive factor (nsf)
Structure: N-ethylmaleimide sensitive factor (nsf-n). Chain: a. Fragment: n-terminal domain of nsf. Engineered: yes. Other_details: this protein is one domain of three in the nsf protomer. Biologically nsf is a hexamer.
Source: Cricetulus griseus. Chinese hamster. Organism_taxid: 10029. Tissue: ovary. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.210     R-free:   0.242
Authors: R.C.Yu,R.Jahn,A.T.Brunger
Key ref:
R.C.Yu et al. (1999). NSF N-terminal domain crystal structure: models of NSF function. Mol Cell, 4, 97. PubMed id: 10445031 DOI: 10.1016/S1097-2765(00)80191-4
Date:
14-May-99     Release date:   18-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18708  (NSF_CRIGR) -  Vesicle-fusing ATPase from Cricetulus griseus
Seq:
Struc: 		 
Seq:
Struc: 		744 a.a.
195 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.6  - vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S1097-2765(00)80191-4 Mol Cell 4:97 (1999)
PubMed id: 10445031  
 
 
NSF N-terminal domain crystal structure: models of NSF function.
R.C.Yu, R.Jahn, A.T.Brunger.
 
  ABSTRACT  
 
N-ethylmaleimide-sensitive factor (NSF) is a hexameric ATPase essential for eukaryotic vesicle fusion. Along with SNAP proteins, it disassembles cis-SNARE complexes upon ATP hydrolysis, preparing SNAREs for trans complex formation. We have determined the crystal structure of the N-terminal domain of NSF (N) to 1.9 A resolution. N contains two subdomains which form a groove that is a likely SNAP interaction site. Unexpectedly, both N subdomains are structurally similar to domains in EF-Tu. Based on this similarity, we propose a model for a large conformational change in NSF that drives SNARE complex disassembly.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Representative Electron Density and Subdomain Interface(A) Density-modified experimental map around Phe-138, contoured at 1.5 σ.(B) 2F[o] − F[c] map of same region as (A), contoured at 1.5 σ and calculated with both model and experimental phases.(C) Stereo rendition of buried water molecules (red spheres) in the interface region between subdomains N[A] (blue) and N[B] (red). Side chains of interface residues are drawn as gray sticks, and helices α1, α2′, and α3′ are rendered as ribbons. Red dashed line indicates disordered residues 162–166. 		Figure 6.
Figure 6. Model of α-SNAP Binding to Groove 3 of NAssuming that the position of D1 is near the C terminus of N, binding of the C terminus of α-SNAP to groove 3 would allow for the penultimate residue of α-SNAP to interact with D1.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (1999, 4, 97-0) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19887446 C.Zhao, E.A.Matveeva, Q.Ren, and S.W.Whiteheart (2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
  J Biol Chem, 285, 761-772.  
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
17634982 E.Bitto, C.A.Bingman, D.A.Kondrashov, J.G.McCoy, R.M.Bannen, G.E.Wesenberg, and G.N.Phillips (2008).
Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family.
  Proteins, 70, 93.
PDB code: 2ifu
17397838 C.Zhao, J.T.Slevin, and S.W.Whiteheart (2007).
Cellular functions of NSF: not just SNAPs and SNAREs.
  FEBS Lett, 581, 2140-2149.  
17302911 J.G.Hanley (2007).
NSF binds calcium to regulate its interaction with AMPA receptor subunit GluR2.
  J Neurochem, 101, 1644-1650.  
16795052 H.G.Martin, J.M.Henley, and G.Meyer (2006).
Novel putative targets of N-ethylmaleimide sensitive fusion protein (NSF) and alpha/beta soluble NSF attachment proteins (SNAPs) include the Pak-binding nucleotide exchange factor betaPIX.
  J Cell Biochem, 99, 1203-1215.  
17018057 K.Shiozawa, N.Goda, T.Shimizu, K.Mizuguchi, N.Kondo, N.Shimozawa, M.Shirakawa, and H.Hiroaki (2006).
The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97.
  FEBS J, 273, 4959-4971.  
15322554 H.Huynh, N.Bottini, S.Williams, V.Cherepanov, L.Musumeci, K.Saito, S.Bruckner, E.Vachon, X.Wang, J.Kruger, C.W.Chow, M.Pellecchia, E.Monosov, P.A.Greer, W.Trimble, G.P.Downey, and T.Mustelin (2004).
Control of vesicle fusion by a tyrosine phosphatase.
  Nat Cell Biol, 6, 831-839.  
14988733 I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, and P.S.Freemont (2004).
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
  EMBO J, 23, 1030-1039.
PDB code: 1s3s
15502339 K.Shiozawa, N.Maita, K.Tomii, A.Seto, N.Goda, Y.Akiyama, T.Shimizu, M.Shirakawa, and H.Hiroaki (2004).
Crystallographic characterization of the N-terminal domain of PEX1.
  Acta Crystallogr D Biol Crystallogr, 60, 2098-2099.  
15328346 K.Shiozawa, N.Maita, K.Tomii, A.Seto, N.Goda, Y.Akiyama, T.Shimizu, M.Shirakawa, and H.Hiroaki (2004).
Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain.
  J Biol Chem, 279, 50060-50068.
PDB code: 1wlf
15469990 V.K.Randhawa, F.S.Thong, D.Y.Lim, D.Li, R.R.Garg, R.Rudge, T.Galli, A.Rudich, and A.Klip (2004).
Insulin and hypertonicity recruit GLUT4 to the plasma membrane of muscle cells by using N-ethylmaleimide-sensitive factor-dependent SNARE mechanisms but different v-SNAREs: role of TI-VAMP.
  Mol Biol Cell, 15, 5565-5573.  
12949490 B.DeLaBarre, and A.T.Brunger (2003).
Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains.
  Nat Struct Biol, 10, 856-863.
PDB code: 1oz4
12941689 J.Furst, R.B.Sutton, J.Chen, A.T.Brunger, and N.Grigorieff (2003).
Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.
  EMBO J, 22, 4365-4374.  
12480933 M.J.Davey, C.Indiani, and M.O'Donnell (2003).
Reconstitution of the Mcm2-7p heterohexamer, subunit arrangement, and ATP site architecture.
  J Biol Chem, 278, 4491-4499.  
12529442 M.Nagahama, M.Suzuki, Y.Hamada, K.Hatsuzawa, K.Tani, A.Yamamoto, and M.Tagaya (2003).
SVIP is a novel VCP/p97-interacting protein whose expression causes cell vacuolation.
  Mol Biol Cell, 14, 262-273.  
12434150 I.Rouiller, B.DeLaBarre, A.P.May, W.I.Weis, A.T.Brunger, R.A.Milligan, and E.M.Wilson-Kubalek (2002).
Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle.
  Nat Struct Biol, 9, 950-957.  
  12438117 M.F.Bader, R.W.Holz, K.Kumakura, and N.Vitale (2002).
Exocytosis: the chromaffin cell as a model system.
  Ann N Y Acad Sci, 971, 178-183.  
12415300 M.J.Davey, D.Jeruzalmi, J.Kuriyan, and M.O'Donnell (2002).
Motors and switches: AAA+ machines within the replisome.
  Nat Rev Mol Cell Biol, 3, 826-835.  
11955072 W.G.Horsnell, G.J.Steel, and A.Morgan (2002).
Analysis of NSF mutants reveals residues involved in SNAP binding and ATPase stimulation.
  Biochemistry, 41, 5230-5235.  
11959502 X.Zhang, F.Beuron, and P.S.Freemont (2002).
Machinery of protein folding and unfolding.
  Curr Opin Struct Biol, 12, 231-238.  
11340056 A.T.Brunger (2001).
Structure of proteins involved in synaptic vesicle fusion in neurons.
  Annu Rev Biophys Biomol Struct, 30, 157-171.  
11297924 A.T.Brunger (2001).
Structural insights into the molecular mechanism of calcium-dependent vesicle-membrane fusion.
  Curr Opin Struct Biol, 11, 163-173.  
11536358 F.Bruckert, T.Casavant, and M.Satre (2001).
Aromatic di-alanine repeats (AdAR) are structural motifs characteristic of the soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) family.
  Proteins, 45, 40-46.  
11250194 G.Mocz, and I.R.Gibbons (2001).
Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases.
  Structure, 9, 93.
PDB code: 1hn5
11593041 J.T.Littleton, R.J.Barnard, S.A.Titus, J.Slind, E.R.Chapman, and B.Ganetzky (2001).
SNARE-complex disassembly by NSF follows synaptic-vesicle fusion.
  Proc Natl Acad Sci U S A, 98, 12233-12238.  
11483507 M.Kato, and W.Wickner (2001).
Ergosterol is required for the Sec18/ATP-dependent priming step of homotypic vacuole fusion.
  EMBO J, 20, 4035-4040.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
10851178 A.T.Brunger (2000).
Structural insights into the molecular mechanism of Ca(2+)-dependent exocytosis.
  Curr Opin Neurobiol, 10, 293-302.  
  10790395 B.Dellinger, R.Felling, and R.W.Ordway (2000).
Genetic modifiers of the Drosophila NSF mutant, comatose, include a temperature-sensitive paralytic allele of the calcium channel alpha1-subunit gene, cacophony.
  Genetics, 155, 203-211.  
11163220 I.Rouiller, V.M.Butel, M.Latterich, R.A.Milligan, and E.M.Wilson-Kubalek (2000).
A major conformational change in p97 AAA ATPase upon ATP binding.
  Mol Cell, 6, 1485-1490.  
11208133 J.A.Ybe, D.E.Wakeham, F.M.Brodsky, and P.K.Hwang (2000).
Molecular structures of proteins involved in vesicle fusion.
  Traffic, 1, 474-479.  
11114503 K.M.Misura, A.P.May, and W.I.Weis (2000).
Protein-protein interactions in intracellular membrane fusion.
  Curr Opin Struct Biol, 10, 662-671.  
11053839 L.M.Rice, T.N.Earnest, and A.T.Brunger (2000).
Single-wavelength anomalous diffraction phasing revisited.
  Acta Crystallogr D Biol Crystallogr, 56, 1413-1420.  
10893253 R.D.Vale (2000).
AAA proteins. Lords of the ring.
  J Cell Biol, 150, F13-F19.  
11163219 X.Zhang, A.Shaw, P.A.Bates, R.H.Newman, B.Gowen, E.Orlova, M.A.Gorman, H.Kondo, P.Dokurno, J.Lally, G.Leonard, H.Meyer, M.van Heel, and P.S.Freemont (2000).
Structure of the AAA ATPase p97.
  Mol Cell, 6, 1473-1484.
PDB code: 1e32
10445030 L.M.Rice, and A.T.Brunger (1999).
Crystal structure of the vesicular transport protein Sec17: implications for SNAP function in SNARE complex disassembly.
  Mol Cell, 4, 85-95.
PDB code: 1qqe
10611286 S.M.Babor, and D.Fass (1999).
Crystal structure of the Sec18p N-terminal domain.
  Proc Natl Acad Sci U S A, 96, 14759-14764.
PDB code: 1cr5
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.

 

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