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PDBsum entry 1om2

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protein Protein-protein interface(s) links
Receptor/oxidoreductase complex PDB id
1om2
Jmol
Contents
Protein chains
95 a.a. *
11 a.a. *
* Residue conservation analysis
PDB id:
1om2
Name: Receptor/oxidoreductase complex
Title: Solution nmr structure of the mitochondrial protein import receptor tom20 from rat in a complex with a presequence peptide derived from rat aldehyde dehydrogenase (aldh)
Structure: Protein (mitochondrial import receptor subunit tom20). Chain: a. Fragment: residues 51-145. Engineered: yes. Other_details: cytosolic domain, limited proteolyzed fragment. Protein (mitochondrial aldehyde dehydrogenase). Chain: b.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organelle: mitochondria. Cellular_location: mitochondrial outer membrane. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The
NMR struc: 20 models
Authors: Y.Abe,T.Shodai,T.Muto,K.Mihara,H.Torii,S.Nishikawa,T.Endo, D.Kohda
Key ref:
Y.Abe et al. (2000). Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell, 100, 551-560. PubMed id: 10721992 DOI: 10.1016/S0092-8674(00)80691-1
Date:
23-Apr-99     Release date:   02-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q62760  (TOM20_RAT) -  Mitochondrial import receptor subunit TOM20 homolog
Seq:
Struc:
145 a.a.
95 a.a.*
Protein chain
Pfam   ArchSchema ?
P11884  (ALDH2_RAT) -  Aldehyde dehydrogenase, mitochondrial
Seq:
Struc:
519 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain B: E.C.1.2.1.3  - Aldehyde dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + NAD+ + H2O = a carboxylate + NADH
aldehyde
+ NAD(+)
+ H(2)O
= carboxylate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrial outer membrane translocase complex   1 term 
  Biological process     intracellular protein transport   2 terms 

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80691-1 Cell 100:551-560 (2000)
PubMed id: 10721992  
 
 
Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20.
Y.Abe, T.Shodai, T.Muto, K.Mihara, H.Torii, S.Nishikawa, T.Endo, D.Kohda.
 
  ABSTRACT  
 
Most mitochondrial proteins are synthesized in the cytosol as precursor proteins with a cleavable N-terminal presequence and are imported into mitochondria. We report here the NMR structure of a general import receptor, rat Tom20, in a complex with a presequence peptide derived from rat aldehyde dehydrogenase. The cytosolic domain of Tom20 forms an all alpha-helical structure with a groove to accommodate the presequence peptide. The bound presequence forms an amphiphilic helical structure with hydrophobic leucines aligned on one side to interact with a hydrophobic patch in the Tom20 groove. Although the positive charges of the presequence are essential for import ability, presequence binding to Tom20 is mediated mainly by hydrophobic rather than ionic interactions.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Structure of Δ50Tom20 in Complex with a Presequence Peptide, pALDH(12–22)(A) Sequence alignment of Δ50Tom20 and corresponding regions of Tom20 from other organisms (human, Caenorhabditis elegans, Neurospora crassa, and yeast Saccharomyces cerevisiae). The two acidic regions and the Q-rich region are shaded in red and yellow, respectively. The TPR motif is shown as a blue box with its consensus amino acids. α helices and flexible regions are drawn as cylinders and broken lines, respectively. The hydrophobic residues constituting the hydrophobic patch in the presequence binding groove are indicated with yellow triangles, and the hydrophilic residues in the periphery of the groove are colored in orange (Gln) and red (Glu) circles.(B) Overlay of the 20 final structures. The residues used for superimposing the different structures are colored in blue (Tom20) and red (presequence peptide), and the other residues are in gray (Tom20) and orange (presequence).(C) Ribbon model of Δ50Tom20 indicating the {^1H}-^15N heteronuclear NOE values (red to white; −0.9 vert, similar +0.9) measured in the absence of the presequence. Smaller NOE values imply faster motions.
Figure 5.
Figure 5. Representation of the Binding Groove of Δ50Tom20 and the Bound Presequence Peptide(A) Molecular surface of Δ50Tom20 (residues 57–124). Hydrophobic residues comprising the hydrophobic patch (Phe^70, Leu^71, Ile^74, Leu^106, Val^109, Leu^110, Thr^113), and Gln (Gln^67, Gln^75, Gln^102, Gln^104, Gln^105, Gln^108, Gln^111, and Gln^112) and Glu (Glu^78 and Glu^79) in the peripheral region are colored in yellow, orange, and red, respectively. The bound peptide is drawn as a tube with sidechains in magenta for Leu, blue for Arg, and cyan for others. N' and C' denote the N and C termini of the peptide, respectively.(B) Same structure viewed from an angle along the arrow shown in (A).
 
  The above figures are reprinted by permission from Cell Press: Cell (2000, 100, 551-560) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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20504278 A.C.Fan, L.M.Gava, C.H.Ramos, and J.C.Young (2010).
Human mitochondrial import receptor Tom70 functions as a monomer.
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Tickled PINK1: mitochondrial homeostasis and autophagy in recessive Parkinsonism.
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Molecular chaperone function of Mia40 triggers consecutive induced folding steps of the substrate in mitochondrial protein import.
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PDB code: 2l0y
20718036 L.de la Cruz, R.Bajaj, S.Becker, and M.Zweckstetter (2010).
The intermembrane space domain of Tim23 is intrinsically disordered with a distinct binding region for presequences.
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20680033 R.Lin, S.Paz, and J.Hiscott (2010).
Tom70 imports antiviral immunity to the mitochondria.
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20435646 W.Q.Li, X.Q.Zhang, C.Xia, Y.Deng, and D.Ye (2010).
MALE GAMETOPHYTE DEFECTIVE 1, encoding the FAd subunit of mitochondrial F1F0-ATP synthase, is essential for pollen formation in Arabidopsis thaliana.
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Tom70 mediates activation of interferon regulatory factor 3 on mitochondria.
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21102411 Y.Sato, H.Shibata, T.Nakatsu, H.Nakano, Y.Kashiwayama, T.Imanaka, and H.Kato (2010).
Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p.
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PDB code: 3ajb
19995731 A.K.Berglund, E.Spånning, H.Biverståhl, G.Maddalo, C.Tellgren-Roth, L.Mäler, and E.Glaser (2009).
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In Silico screening for functional candidates amongst hypothetical proteins.
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A novel intermembrane space-targeting signal docks cysteines onto Mia40 during mitochondrial oxidative folding.
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Roles of Tom70 in import of presequence-containing mitochondrial proteins.
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19581297 J.Li, X.Qian, J.Hu, and B.Sha (2009).
Molecular chaperone Hsp70/Hsp90 prepares the mitochondrial outer membrane translocon receptor Tom71 for preprotein loading.
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PDB codes: 3fp2 3fp3 3fp4
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PDB code: 2fbn
19028997 R.F.Waller, C.Jabbour, N.C.Chan, N.Celik, V.A.Likic, T.D.Mulhern, and T.Lithgow (2009).
Evidence of a reduced and modified mitochondrial protein import apparatus in microsporidian mitosomes.
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19453276 T.Endo, and K.Yamano (2009).
Multiple pathways for mitochondrial protein traffic.
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18369189 C.J.McCleverty, L.Columbus, A.Kreusch, and S.A.Lesley (2008).
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PDB codes: 2vkj 2vko
18537026 E.P.Neve, and M.Ingelman-Sundberg (2008).
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18551319 J.M.Kang, H.I.Cheun, J.Kim, S.U.Moon, S.J.Park, T.S.Kim, W.M.Sohn, and B.K.Na (2008).
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18063580 K.Yamano, Y.Yatsukawa, M.Esaki, A.E.Hobbs, R.E.Jensen, and T.Endo (2008).
Tom20 and Tom22 share the common signal recognition pathway in mitochondrial protein import.
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18174896 N.Bolender, A.Sickmann, R.Wagner, C.Meisinger, and N.Pfanner (2008).
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17596514 M.K.Bhangoo, S.Tzankov, A.C.Fan, K.Dejgaard, D.Y.Thomas, and J.C.Young (2007).
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17446895 O.Emanuelsson, S.Brunak, G.von Heijne, and H.Nielsen (2007).
Locating proteins in the cell using TargetP, SignalP and related tools.
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17998403 S.Kutik, B.Guiard, H.E.Meyer, N.Wiedemann, and N.Pfanner (2007).
Cooperation of translocase complexes in mitochondrial protein import.
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17948058 T.Saitoh, M.Igura, T.Obita, T.Ose, R.Kojima, K.Maenaka, T.Endo, and D.Kohda (2007).
Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states.
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PDB codes: 2v1s 2v1t
17263664 W.Neupert, and J.M.Herrmann (2007).
Translocation of proteins into mitochondria.
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Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC.
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PDB code: 2e0g
17998537 Y.Zhang, and D.C.Chan (2007).
Structural basis for recruitment of mitochondrial fission complexes by Fis1.
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PDB codes: 2pqn 2pqr
17008120 A.H.Millar, J.Whelan, and I.Small (2006).
Recent surprises in protein targeting to mitochondria and plastids.
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16461275 A.J.Perry, J.M.Hulett, V.A.Likić, T.Lithgow, and P.R.Gooley (2006).
Convergent evolution of receptors for protein import into mitochondria.
  Curr Biol, 16, 221-229.
PDB code: 1zu2
17088320 A.Mukhopadhyay, C.S.Yang, and H.Weiner (2006).
Binding of mitochondrial leader sequences to Tom20 assessed using a bacterial two-hybrid system shows that hydrophobic interactions are essential and that some mutated leaders that do not bind Tom20 can still be imported.
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16616497 C.de Marcos-Lousa, D.P.Sideris, and K.Tokatlidis (2006).
Translocation of mitochondrial inner-membrane proteins: conformation matters.
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16914527 J.M.Harper, M.H.Huynh, I.Coppens, F.Parussini, S.Moreno, and V.B.Carruthers (2006).
A cleavable propeptide influences Toxoplasma infection by facilitating the trafficking and secretion of the TgMIC2-M2AP invasion complex.
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16857931 P.Dolezal, V.Likic, J.Tachezy, and T.Lithgow (2006).
Evolution of the molecular machines for protein import into mitochondria.
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17099692 R.Albrecht, P.Rehling, A.Chacinska, J.Brix, S.A.Cadamuro, R.Volkmer, B.Guiard, N.Pfanner, and K.Zeth (2006).
The Tim21 binding domain connects the preprotein translocases of both mitochondrial membranes.
  EMBO Rep, 7, 1233-1238.
PDB code: 2ciu
16546069 R.Lister, and J.Whelan (2006).
Mitochondrial protein import: convergent solutions for receptor structure.
  Curr Biol, 16, R197-R199.  
16892083 W.C.Cheng, S.B.Berman, I.Ivanovska, E.A.Jonas, S.J.Lee, Y.Chen, L.K.Kaczmarek, F.Pineda, and J.M.Hardwick (2006).
Mitochondrial factors with dual roles in death and survival.
  Oncogene, 25, 4697-4705.  
16767096 Y.Wu, and B.Sha (2006).
Crystal structure of yeast mitochondrial outer membrane translocon member Tom70p.
  Nat Struct Mol Biol, 13, 589-593.
PDB code: 2gw1
16331427 A.J.Perry, J.M.Hulett, T.Lithgow, and P.R.Gooley (2005).
1H, 13C and 15N resonance assignments of the cytosolic domain of Tom20 from Arabidopsis thaliana.
  J Biomol NMR, 33, 198.  
15634341 C.G.Wilson, T.Kajander, and L.Regan (2005).
The crystal structure of NlpI. A prokaryotic tetratricopeptide repeat protein with a globular fold.
  FEBS J, 272, 166-179.
PDB code: 1xnf
15882268 I.Santamaría, D.Alvarez-Hernández, R.Jofré, J.R.Polo, J.Menárguez, and J.B.Cannata-Andía (2005).
Progression of secondary hyperparathyroidism involves deregulation of genes related to DNA and RNA stability.
  Kidney Int, 67, 2267-2279.  
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Crystallization and preliminary X-ray analysis of mitochondrial presequence receptor Tom20 in complexes with a presequence from aldehyde dehydrogenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 514-517.  
15605252 X.Chen, R.P.Moerschell, D.A.Pearce, D.D.Ramanan, and F.Sherman (2005).
Enhanced mitochondrial degradation of yeast cytochrome c with amphipathic structures.
  Curr Genet, 47, 67-83.  
15473843 C.M.Koehler (2004).
New developments in mitochondrial assembly.
  Annu Rev Cell Dev Biol, 20, 309-335.  
15294046 D.A.Hood, and A.M.Joseph (2004).
Mitochondrial assembly: protein import.
  Proc Nutr Soc, 63, 293-300.  
15075277 J.Slapeta, and J.S.Keithly (2004).
Cryptosporidium parvum mitochondrial-type HSP70 targets homologous and heterologous mitochondria.
  Eukaryot Cell, 3, 483-494.  
15337763 M.Esaki, H.Shimizu, T.Ono, H.Yamamoto, T.Kanamori, S.Nishikawa, and T.Endo (2004).
Mitochondrial protein import. Requirement of presequence elements and tom components for precursor binding to the TOM complex.
  J Biol Chem, 279, 45701-45707.  
14699115 M.Yano, K.Terada, and M.Mori (2004).
Mitochondrial import receptors Tom20 and Tom22 have chaperone-like activity.
  J Biol Chem, 279, 10808-10813.  
15523480 N.Pfanner, N.Wiedemann, C.Meisinger, and T.Lithgow (2004).
Assembling the mitochondrial outer membrane.
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14973134 N.Wiedemann, A.E.Frazier, and N.Pfanner (2004).
The protein import machinery of mitochondria.
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15232570 P.Rehling, K.Brandner, and N.Pfanner (2004).
Mitochondrial import and the twin-pore translocase.
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15215243 S.A.Graf, S.E.Haigh, E.D.Corson, and O.S.Shirihai (2004).
Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me).
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15316022 T.Beddoe, S.R.Bushell, M.A.Perugini, T.Lithgow, T.D.Mulhern, S.P.Bottomley, and J.Rossjohn (2004).
A biophysical analysis of the tetratricopeptide repeat-rich mitochondrial import receptor, Tom70, reveals an elongated monomer that is inherently flexible, unstable, and unfolds via a multistate pathway.
  J Biol Chem, 279, 46448-46454.  
14985332 Y.Nakamura, H.Suzuki, M.Sakaguchi, and K.Mihara (2004).
Targeting and assembly of rat mitochondrial translocase of outer membrane 22 (TOM22) into the TOM complex.
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14532110 A.Chacinska, P.Rehling, B.Guiard, A.E.Frazier, A.Schulze-Specking, N.Pfanner, W.Voos, and C.Meisinger (2003).
Mitochondrial translocation contact sites: separation of dynamic and stabilizing elements in formation of a TOM-TIM-preprotein supercomplex.
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12660160 A.Yamashita, K.Maeda, and Y.Maéda (2003).
Crystal structure of CapZ: structural basis for actin filament barbed end capping.
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PDB code: 1izn
14557549 K.J.Walters, P.J.Lech, A.M.Goh, Q.Wang, and P.M.Howley (2003).
DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a.
  Proc Natl Acad Sci U S A, 100, 12694-12699.
PDB codes: 1oqy 1qze
12899691 M.San Miguel, R.Marrington, P.M.Rodger, A.Rodger, and C.Robinson (2003).
An Escherichia coli twin-arginine signal peptide switches between helical and unstructured conformations depending on the hydrophobicity of the environment.
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AIP is a mitochondrial import mediator that binds to both import receptor Tom20 and preproteins.
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Mitochondrial targeting of normal and mutant protoporphyrinogen oxidase.
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Bipartite signals mediate subcellular targeting of tail-anchored membrane proteins in Saccharomyces cerevisiae.
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12640110 T.Stan, J.Brix, J.Schneider-Mergener, N.Pfanner, W.Neupert, and D.Rapaport (2003).
Mitochondrial protein import: recognition of internal import signals of BCS1 by the TOM complex.
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Ligand discrimination by TPR domains. Relevance and selectivity of EEVD-recognition in Hsp70 x Hop x Hsp90 complexes.
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12185844 A.Chacinska, N.Pfanner, and C.Meisinger (2002).
How mitochondria import hydrophilic and hydrophobic proteins.
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12198123 A.J.Johnston, J.Hoogenraad, D.A.Dougan, K.N.Truscott, M.Yano, M.Mori, N.J.Hoogenraad, and M.T.Ryan (2002).
Insertion and assembly of human tom7 into the preprotein translocase complex of the outer mitochondrial membrane.
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11967360 A.Mukhopadhyay, P.Hammen, M.Waltner-Law, and H.Weiner (2002).
Timing and structural consideration for the processing of mitochondrial matrix space proteins by the mitochondrial processing peptidase (MPP).
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The human silent information regulator (Sir)2 homologue hSIRT3 is a mitochondrial nicotinamide adenine dinucleotide-dependent deacetylase.
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A novel in vitro system for simultaneous import of precursor proteins into mitochondria and chloroplasts.
  Plant J, 30, 213-220.  
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Rapid regulation of steroidogenesis by mitochondrial protein import.
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Mitochondrial protein import: two membranes, three translocases.
  Curr Opin Cell Biol, 14, 400-411.  
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Analysis of interactions between domains of a small heat shock protein, Hsp30 of Neurospora crassa.
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11684692 R.D.Moir, K.V.Puglia, and I.M.Willis (2002).
Autoinhibition of TFIIIB70 binding by the tetratricopeptide repeat-containing subunit of TFIIIC.
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A gain-of-function mutation in the second tetratricopeptide repeat of TFIIIC131 relieves autoinhibition of Brf1 binding.
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A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
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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.