PDBsum entry 1svo

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protein metals Protein-protein interface(s) links
Viral protein PDB id
Jmol PyMol
Protein chains
362 a.a. *
_ZN ×2
Waters ×188
* Residue conservation analysis
PDB id:
Name: Viral protein
Title: Structure of sv40 large t antigen helicase domain
Structure: Large t antigen. Chain: a, b. Fragment: helicase domain. Engineered: yes
Source: Simian virus 40. Organism_taxid: 10633. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
2.60Å     R-factor:   0.233     R-free:   0.271
Authors: D.Gai,R.Zhao,C.V.Finkielstein,X.S.Chen
Key ref:
D.Gai et al. (2004). Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell, 119, 47-60. PubMed id: 15454080 DOI: 10.1016/j.cell.2004.09.017
29-Mar-04     Release date:   19-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P03070  (LT_SV40) -  Large T antigen
708 a.a.
362 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   1 term 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1016/j.cell.2004.09.017 Cell 119:47-60 (2004)
PubMed id: 15454080  
Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen.
D.Gai, R.Zhao, D.Li, C.V.Finkielstein, X.S.Chen.
The large tumor antigen (LTag) of simian virus 40, an AAA(+) protein, is a hexameric helicase essential for viral DNA replication in eukaryotic cells. LTag functions as an efficient molecular machine powered by ATP binding and hydrolysis for origin DNA melting and replication fork unwinding. To understand how ATP binding and hydrolysis are coupled to conformational changes, we have determined high-resolution structures ( approximately 1.9 A) of LTag hexamers in distinct nucleotide binding states. The structural differences of LTag in various nucleotide states detail the molecular mechanisms of conformational changes triggered by ATP binding/hydrolysis and reveal a potential mechanism of concerted nucleotide binding and hydrolysis. During these conformational changes, the angles and orientations between domains of a monomer alter, creating an "iris"-like motion in the hexamer. Additionally, six unique beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.
  Selected figure(s)  
Figure 1.
Figure 1. An Overview of the Nt-Free Structure of a LTag Monomer and its Hexamer(A) The LTag domain structure in ribbon diagram. D1 is the N-terminal domain, D2 the AAA+ domain, and D3 the C-terminal α-helical domain. The thin red line shows the border between D2 and D3. The N and C termini are labeled as N and C. ATP binding P loop and the Nt binding pocket (Nt pocket) for binding the base are indicated by arrows.(B) The C-terminal view of a LTag hexamer structure along the hexameric axis, with the D2/D3 on top.
Figure 2.
Figure 2. The Changes of Channel Openings and Hexamerization Interfaces of LTag Hexamers in Three Nt Binding States, Viewing from the C-Terminal EndTo provide a clearer view of the Nt binding cleft at the hexamerization interface, only the D2/D3 parts of the hexamer are shown. Each of the six monomers is in a different color. (A) The ATP bound hexamer structure. The six ATPs at the cleft between two monomers are in pink. (B) The ADP bound hexamer structure, showing ADP (pink) at the cleft. (C) The Nt-free hexamer structure. (D) A close-up view of the cleft between two neighboring monomers (in green and cyan) of the Nt-free structure. (E) The same view of the cleft between two neighbors from two different Nt bound structures: the Nt-free structure (in green and cyan) and the ATP bound structure (in pink and gold), showing a narrowing of the cleft when ATP is bound. The bound ATP and Mg^2+ are in purple.
  The above figures are reprinted by permission from Cell Press: Cell (2004, 119, 47-60) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 3vkg 3vkh
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PDB code: 3f8t
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PDB codes: 3hte 3hws
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PDB code: 3f9v
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PDB codes: 2vhc 2vhj 2vhq 2vht 2vhu
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Mcm subunits can assemble into two different active unwinding complexes.
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PDB codes: 3bgw 3bh0
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Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
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PDB codes: 3cf0 3cf1 3cf2 3cf3
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Subunit organization of Mcm2-7 and the unequal role of active sites in ATP hydrolysis and viability.
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Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
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18754676 R.J.Fletcher, J.Shen, L.G.Holden, and X.S.Chen (2008).
Identification of amino acids important for the biochemical activity of Methanothermobacter thermautotrophicus MCM.
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Functional conservation of beta-hairpin DNA binding domains in the Mcm protein of Methanobacterium thermoautotrophicum and the Mcm5 protein of Saccharomyces cerevisiae.
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Simian virus 40 DNA replication is dependent on an interaction between topoisomerase I and the C-terminal end of T antigen.
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Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase.
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The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
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Ataxia telangiectasia-mutated damage-signaling kinase- and proteasome-dependent destruction of Mre11-Rad50-Nbs1 subunits in Simian virus 40-infected primate cells.
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17596312 A.Fradet-Turcotte, C.Vincent, S.Joubert, P.A.Bullock, and J.Archambault (2007).
Quantitative analysis of the binding of simian virus 40 large T antigen to DNA.
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Model for T-antigen-dependent melting of the simian virus 40 core origin based on studies of the interaction of the beta-hairpin with DNA.
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Biochemical, biophysical, and proteomic approaches to study DNA helicases.
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Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors.
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PDB code: 2v9p
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The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA.
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PDB codes: 2if9 2ntc
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Cell cycle regulation of DNA replication.
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Molecular chaperones and protein quality control.
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Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
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PDB codes: 2ipr 2itj 2itl 2nl8
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Mechanism of DNA translocation in a replicative hexameric helicase.
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PDB code: 2gxa
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DNA replication in the archaea.
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16679413 E.R.Jenkinson, and J.P.Chong (2006).
Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert.
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Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor.
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PDB code: 2ht1
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Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
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PDB code: 2fuf
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The chromosome replication machinery of the archaeon Sulfolobus solfataricus.
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Adaptor protein controlled oligomerization activates the AAA+ protein ClpC.
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Mechanochemistry of transcription termination factor Rho.
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Evolutionary relationships and structural mechanisms of AAA+ proteins.
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Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling.
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PDB code: 2hcb
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A helicase staircase.
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Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.
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PDB codes: 2c96 2c98 2c99 2c9c
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Replicative helicases: a staircase with a twist.
  Curr Biol, 16, R844-R847.  
16973614 N.Joly, J.Schumacher, and M.Buck (2006).
Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator.
  J Biol Chem, 281, 34997-35007.  
17060327 P.M.Matias, S.Gorynia, P.Donner, and M.A.Carrondo (2006).
Crystal structure of the human AAA+ protein RuvBL1.
  J Biol Chem, 281, 38918-38929.
PDB code: 2c9o
16893956 S.Castella, D.Burgin, and C.M.Sanders (2006).
Role of ATP hydrolysis in the DNA translocase activity of the bovine papillomavirus (BPV-1) E1 helicase.
  Nucleic Acids Res, 34, 3731-3741.  
16738139 S.Castella, G.Bingham, and C.M.Sanders (2006).
Common determinants in DNA melting and helicase-catalysed DNA unwinding by papillomavirus replication protein E1.
  Nucleic Acids Res, 34, 3008-3019.  
16431356 S.E.Ades (2006).
AAA+ molecular machines: firing on all cylinders.
  Curr Biol, 16, R46-R48.  
16670085 S.S.Patel, and I.Donmez (2006).
Mechanisms of helicases.
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17082766 V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, and D.M.Mueller (2006).
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase.
  EMBO J, 25, 5433-5442.
PDB code: 2hld
16951253 W.Lilyestrom, M.G.Klein, R.Zhang, A.Joachimiak, and X.S.Chen (2006).
Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor.
  Genes Dev, 20, 2373-2382.
PDB code: 2h1l
17110927 X.Jiang, V.Klimovich, A.I.Arunkumar, E.B.Hysinger, Y.Wang, R.D.Ott, G.D.Guler, B.Weiner, W.J.Chazin, and E.Fanning (2006).
Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex.
  EMBO J, 25, 5516-5526.  
16237435 A.Martin, T.A.Baker, and R.T.Sauer (2005).
Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines.
  Nature, 437, 1115-1120.  
16193069 A.Scott, H.Y.Chung, M.Gonciarz-Swiatek, G.C.Hill, F.G.Whitby, J.Gaspar, J.M.Holton, R.Viswanathan, S.Ghaffarian, C.P.Hill, and W.I.Sundquist (2005).
Structural and mechanistic studies of VPS4 proteins.
  EMBO J, 24, 3658-3669.
PDB code: 1xwi
16116441 A.T.McGeoch, M.A.Trakselis, R.A.Laskey, and S.D.Bell (2005).
Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism.
  Nat Struct Mol Biol, 12, 756-762.  
15989952 G.L.Hersch, R.E.Burton, D.N.Bolon, T.A.Baker, and R.T.Sauer (2005).
Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine.
  Cell, 121, 1017-1027.  
15870080 G.Ondrovicová, T.Liu, K.Singh, B.Tian, H.Li, O.Gakh, D.Perecko, J.Janata, Z.Granot, J.Orly, E.Kutejová, and C.K.Suzuki (2005).
Cleavage site selection within a folded substrate by the ATP-dependent lon protease.
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15901724 H.Kawakami, K.Keyamura, and T.Katayama (2005).
Formation of an ATP-DnaA-specific initiation complex requires DnaA Arginine 285, a conserved motif in the AAA+ protein family.
  J Biol Chem, 280, 27420-27430.  
15989953 J.Hinnerwisch, W.A.Fenton, K.J.Furtak, G.W.Farr, and A.L.Horwich (2005).
Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation.
  Cell, 121, 1029-1041.  
15840563 J.Lísal, and R.Tuma (2005).
Cooperative mechanism of RNA packaging motor.
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15834422 J.Lísal, T.T.Lam, D.E.Kainov, M.R.Emmett, A.G.Marshall, and R.Tuma (2005).
Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states.
  Nat Struct Mol Biol, 12, 460-466.  
16142223 J.P.Chong (2005).
Learning to unwind.
  Nat Struct Mol Biol, 12, 734-736.  
16061814 J.Shen, D.Gai, A.Patrick, W.B.Greenleaf, and X.S.Chen (2005).
The roles of the residues on the channel beta-hairpin and loop structures of simian virus 40 hexameric helicase.
  Proc Natl Acad Sci U S A, 102, 11248-11253.  
16304143 P.W.White, A.M.Faucher, M.J.Massariol, E.Welchner, J.Rancourt, M.Cartier, and J.Archambault (2005).
Biphenylsulfonacetic acid inhibitors of the human papillomavirus type 6 E1 helicase inhibit ATP hydrolysis by an allosteric mechanism involving tyrosine 486.
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16221679 R.J.Fletcher, J.Shen, Y.Gómez-Llorente, C.S.Martín, J.M.Carazo, and X.S.Chen (2005).
Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM.
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15829969 S.J.Riedl, W.Li, Y.Chao, R.Schwarzenbacher, and Y.Shi (2005).
Structure of the apoptotic protease-activating factor 1 bound to ADP.
  Nature, 434, 926-933.
PDB code: 1z6t
16285920 S.Schuck, and A.Stenlund (2005).
Assembly of a double hexameric helicase.
  Mol Cell, 20, 377-389.  
16002295 T.S.Takahashi, D.B.Wigley, and J.C.Walter (2005).
Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase.
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16306270 Z.Bu, R.Biehl, M.Monkenbusch, D.Richter, and D.J.Callaway (2005).
Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy.
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15454074 B.F.Eichman, and E.Fanning (2004).
The power of pumping together; deconstructing the engine of a DNA replication machine.
  Cell, 119, 3-4.  
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.