PDBsum entry 1ckt

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protein dna_rna ligands links
Gene regulation/DNA PDB id
Protein chain
71 a.a. *
Waters ×74
* Residue conservation analysis
PDB id:
Name: Gene regulation/DNA
Title: Crystal structure of hmg1 domain a bound to a cisplatin-modi duplex
Structure: DNA (5'-d( Cp Cp (5Iu) p Cp Tp Cp Tp Gp Gp Ap Cp Cp Tp Tp Cp C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Gp Gp Ap Ap Gp Gp Tp Cp Cp Ap Gp Ap Gp 3'). Chain: c. Engineered: yes. High mobility group 1 protein.
Source: Synthetic: yes. Rattus norvegicus. Norway rat. Organism_taxid: 10116. Strain: soragye-dawley. Tissue: liver. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
2.50Å     R-factor:   0.238     R-free:   0.239
Authors: U.-M.Ohndorf,M.A.Rould,C.O.Pabo,S.J.Lippard
Key ref:
U.M.Ohndorf et al. (1999). Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature, 399, 708-712. PubMed id: 10385126 DOI: 10.1038/21460
23-Apr-99     Release date:   30-Jun-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P63159  (HMGB1_RAT) -  High mobility group protein B1
215 a.a.
71 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biochemical function     DNA binding     1 term  


DOI no: 10.1038/21460 Nature 399:708-712 (1999)
PubMed id: 10385126  
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.
U.M.Ohndorf, M.A.Rould, Q.He, C.O.Pabo, S.J.Lippard.
The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered structure attracts high-mobility-group domain (HMG) and other proteins. This binding of HMG-domain proteins to cisplatin-modified DNA has been postulated to mediate the antitumour properties of the drug. Many HMG-domain proteins recognize altered DNA structures such as four-way junctions and cisplatin-modified DNA, but until now the molecular basis for this recognition was unknown. Here we describe mutagenesis, hydroxyl-radical footprinting and X-ray studies that elucidate the structure of a 1:1 cisplatin-modified DNA/HMG-domain complex. Domain A of the structure-specific HMG-domain protein HMG1 binds to the widened minor groove of a 16-base-pair DNA duplex containing a adduct. The DNA is strongly kinked at a hydrophobic notch created at the platinum-DNA crosslink and protein binding extends exclusively to the 3' side of the platinated strand. A phenylalanine residue at position 37 intercalates into a hydrophobic notch created at the platinum crosslinked d(GpG) site and binding of the domain is dramatically reduced in a mutant in which alanine is substituted for phenylalanine at this position.
  Selected figure(s)  
Figure 1.
Figure 1: Primary structure and features of the complex between the non-sequence-specific domain A of HMG1 and cisplatin-modified DNA. a, Sequence of DNA used here; asterisks, nucleotides crosslinked by cisplatin. Nucleotides contacted by the protein are in bold type. b, Alignment of selected members of the two subfamilies of HMG-domain proteins^30, based on primary sequence and structural superposition. Shaded boxes represent -helices and solid lines indicate loops. The top group are a representative set of structure-specific HMG domains and the bottom group are sequence-specific proteins. The HMG1 domain A sequence and numbering shown correspond to the residues located and refined in the crystal structure. Residues that contact DNA in structurally characterized complexes are highlighted. Amino acids at positions equivalent to residue 37 of HMG1 are boxed. c, A simulated annealing omit map (starting temperature, 2,000 K), contoured at the 1.1 level, in the region of the cisplatin–DNA adduct and showing the localized bend at the platination site and the intercalated Phe 37 side chain. For computing this (F[o] - F[c]) electron density map, residues 36–38 and bases T[7]–G[9], C[24]–A[26] were omitted. d, Overall structure of the complex. The protein backbone is shown in yellow, the intercalating Phe 37 residue as van der Waals spheres, and the DNA in red and blue with the cis -[Pt(NH[3])[2]{d(GpG)-N7(G[8]),-N7(G[9])}] intrastrand adduct in green. Numbers indicate the first (N terminus) and last (C terminus) ordered residues in the crystal structure. Main-chain torsion angles for all non-glycine residues fall within energetically favourable Ramachandran boundaries.
Figure 3.
Figure 3: The platinum–DNA crosslink and protein–DNA interactions. a, Diagram summarizing all HMG domain–DNA contacts. Solid lines, hydrogen bonds or salt bridges; dashed lines, van der Waals contacts; mc, main chain; and w, water molecule. The wedge indicates the Phe-37 intercalation site. b, Expanded view ofprotein–DNA interactions at the site of platination. The aromatic rings of Phe 37and G[8] pack edge-to-face with a dihedral angle of 74°. The main-chain carbonyl group of Phe 37 is within hydrogen-bonding distance (2.9 Å) of the exocyclic amino group of G[9]. As predicted^7, Ser 41 is involved in a very tight hydrogen-bonding contact with N3 of A[10]. c, Superposition of crystallographically determined cisplatin–{d(GpG)} intrastrand crosslinks in the present structure (yellow), the equivalent site in the structure of a single-stranded stranded cis -[Pt(NH[3])[2]{d(pGpG)}] platinated dinucleotide^17 (blue, left), and the site in a cisplatin-modified DNA dodecamer duplex^14 (red, right), portraying dihedral angles between the two coordinated guanine bases of 75°, 77° and 30°, respectively, as calculated by the program QUANTA 4.1 (Molecular Simulations).
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 399, 708-712) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3tq6
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High-mobility group box 1, oxidative stress, and disease.
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The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.
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PDB code: 3tmm
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Mice with cisplatin and oxaliplatin-induced painful neuropathy develop distinct early responses to thermal stimuli.
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DNA interactions and photocatalytic strand cleavage by artificial nucleases based on water-soluble gold(III) porphyrins.
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HMGB1/2 can target DNA for illegitimate cleavage by the RAG1/2 complex.
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19236006 N.T.Sebastian, E.M.Bystry, N.A.Becker, and L.J.Maher (2009).
Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues.
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Protein recognition of platinated DNA.
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19726587 S.Ray, and A.Grove (2009).
The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends.
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19360789 S.S.Lange, and K.M.Vasquez (2009).
HMGB1: the jack-of-all-trades protein is a master DNA repair mechanic.
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19446504 S.S.Lange, M.C.Reddy, and K.M.Vasquez (2009).
Human HMGB1 directly facilitates interactions between nucleotide excision repair proteins on triplex-directed psoralen interstrand crosslinks.
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19304746 T.A.Gangelhoff, P.S.Mungalachetty, J.C.Nix, and M.E.Churchill (2009).
Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.
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PDB code: 3fgh
18777181 T.Suchánková, M.Vojtísková, J.Reedijk, V.Brabec, and J.Kaspárková (2009).
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18702462 J.Qian, D.Cuerrier, P.L.Davies, Z.Li, J.C.Powers, and R.L.Campbell (2008).
Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.
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PDB codes: 2r9c 2r9f
18413230 J.Zimmerman, and L.J.Maher (2008).
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Biology of testicular germ cell tumors.
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17226794 G.Hoppe, M.E.Rayborn, and J.E.Sears (2007).
Diurnal rhythm of the chromatin protein Hmgb1 in rat photoreceptors is under circadian regulation.
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Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1.
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PDB code: 2hdz
17704160 J.Malina, O.Novakova, M.Vojtiskova, G.Natile, and V.Brabec (2007).
Conformation of DNA GG intrastrand cross-link of antitumor oxaliplatin and its enantiomeric analog.
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17462578 L.Mollica, F.De Marchis, A.Spitaleri, C.Dallacosta, D.Pennacchini, M.Zamai, A.Agresti, L.Trisciuoglio, G.Musco, and M.E.Bianchi (2007).
Glycyrrhizin binds to high-mobility group box 1 protein and inhibits its cytokine activities.
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17264930 M.J.Hannon (2007).
Supramolecular DNA recognition.
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17384639 M.L.Qi, K.Tagawa, Y.Enokido, N.Yoshimura, Y.Wada, K.Watase, S.Ishiura, I.Kanazawa, J.Botas, M.Saitoe, E.E.Wanker, and H.Okazawa (2007).
Proteome analysis of soluble nuclear proteins reveals that HMGB1/2 suppress genotoxic stress in polyglutamine diseases.
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17024406 M.Pavelka, and J.V.Burda (2007).
Pt-bridges in various single-strand and double-helix DNA sequences. DFT and MP2 study of the cisplatin coordination with guanine, adenine, and cytosine.
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17979840 M.T.Lotze, H.J.Zeh, A.Rubartelli, L.J.Sparvero, A.A.Amoscato, N.R.Washburn, M.E.Devera, X.Liang, M.Tör, and T.Billiar (2007).
The grateful dead: damage-associated molecular pattern molecules and reduction/oxidation regulate immunity.
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17409541 S.Kobayashi, and Y.Koyama (2007).
Topological differences in the interaction of human DNA topoisomerase I with DNA-histone complexes modified by cis- and trans-DDP.
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17900616 S.Sharma, P.Gong, B.Temple, D.Bhattacharyya, N.V.Dokholyan, and S.G.Chaney (2007).
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics.
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High mobility group box I (HMGB1) release from tumor cells after treatment: implications for development of targeted chemoimmunotherapy.
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17409540 Y.Koyama, S.Kikuchi, S.Nakagawa, and S.Kobayashi (2007).
Dissociation of DNA from histone by reaction of anti-cancer drug cis-diamminedichloroplatinum(II) with DNA-histone complexes used as cellular model.
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17497831 Y.Wu, D.Bhattacharyya, C.L.King, I.Baskerville-Abraham, S.H.Huh, G.Boysen, J.A.Swenberg, B.Temple, S.L.Campbell, and S.G.Chaney (2007).
Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link.
  Biochemistry, 46, 6477-6487.
PDB codes: 2npw 2nq0 2nq1 2nq4
16807967 H.K.Liu, F.Wang, J.A.Parkinson, J.Bella, and P.J.Sadler (2006).
Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes.
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16791311 K.Spiegel, and A.Magistrato (2006).
Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations.
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16953416 M.Hägerlöf, P.Papsai, C.S.Chow, and S.K.Elmroth (2006).
More pronounced salt dependence and higher reactivity for platination of the hairpin r(CGCGUUGUUCGCG) compared with d(CGCGTTGTTCGCG).
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16698780 M.Zacharias (2006).
Minor groove deformability of DNA: a molecular dynamics free energy simulation study.
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16163486 P.Widlak, M.Pietrowska, and J.Lanuszewska (2006).
The role of chromatin proteins in DNA damage recognition and repair.
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16720266 S.Burdette (2006).
trans-Platinum reporting for duty.
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A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding.
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Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
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PDB codes: 1wto 1wtp 1wtq 1wtr 1wtv 1wtw 1wtx 1xyi
15744707 J.K.Lau, and D.V.Deubel (2005).
Loss of amine from platinum(II) complexes: implications for cisplatin inactivation, storage, and resistance.
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Profiling of proteins associated with cisplatin resistance in ovarian cancer cells.
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15997435 M.Benedetti, L.G.Marzilli, and G.Natile (2005).
Rotamer stability in cis-[Pt(diA)G2] complexes (diA = diamine derivative and G = guanine derivative) mediated by carrier-ligand amine stereochemistry as revealed by circular dichroism spectroscopy.
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Recognition and processing of cisplatin- and oxaliplatin-DNA adducts.
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Conformation, protein recognition and repair of DNA interstrand and intrastrand cross-links of antitumor trans-[PtCl2(NH3)(thiazole)].
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15899848 Y.Dai, B.Wong, Y.M.Yen, M.A.Oettinger, J.Kwon, and R.C.Johnson (2005).
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The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains.
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Evidence for involvement of HMGB1 protein in human DNA mismatch repair.
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15286730 J.Vakkila, and M.T.Lotze (2004).
Inflammation and necrosis promote tumour growth.
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The DNA architectural protein HMGB1 facilitates RTA-mediated viral gene expression in gamma-2 herpesviruses.
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12672494 A.Agresti, and M.E.Bianchi (2003).
HMGB proteins and gene expression.
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TOX defines a conserved subfamily of HMG-box proteins.
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Activation of trans geometry in bifunctional mononuclear platinum complexes by a piperidine ligand. Mechanistic studies on antitumor action.
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The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity.
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12835671 J.R.Masters, and B.Köberle (2003).
Curing metastatic cancer: lessons from testicular germ-cell tumours.
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New clues for platinum antitumor chemistry: kinetically controlled metal binding to DNA.
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Cisplatin sensitivity in Hmbg1-/- and Hmbg1+/+ mouse cells.
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DNA-protein cross-linking by trans-[PtCl(2)(E-iminoether)(2)]. A concept for activation of the trans geometry in platinum antitumor complexes.
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12728270 S.D.Cline, and P.C.Hanawalt (2003).
Who's on first in the cellular response to DNA damage?
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12377787 A.P.Silverman, W.Bu, S.M.Cohen, and S.J.Lippard (2002).
2.4-A crystal structure of the asymmetric platinum complex [Pt(ammine)(cyclohexylamine)]2+ bound to a dodecamer DNA duplex.
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PDB code: 1lu5
11733188 E.A.Pasheva, I.Ugrinova, N.C.Spassovska, and I.G.Pashev (2002).
The binding affinity of HMG1 protein to DNA modified by cis-platin and its analogs correlates with their antitumor activity.
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12226099 J.Kasparkova, J.Zehnulova, N.Farrell, and V.Brabec (2002).
DNA interstrand cross-links of the novel antitumor trinuclear platinum complex BBR3464. Conformation, recognition by high mobility group domain proteins, and nucleotide excision repair.
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The DNA architectural protein HMGB1 displays two distinct modes of action that promote enhanceosome assembly.
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12087174 K.Stehlikova, H.Kostrhunova, J.Kasparkova, and V.Brabec (2002).
DNA bending and unwinding due to the major 1,2-GG intrastrand cross-link formed by antitumor cis-diamminedichloroplatinum(II) are flanking-base independent.
  Nucleic Acids Res, 30, 2894-2898.  
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Chiral discrimination in platinum anticancer drugs.
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12237082 V.Brabec, and J.Kasparkova (2002).
Molecular aspects of resistance to antitumor platinum drugs.
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11954836 W.H.Fang, Y.M.Yao, Z.G.Shi, Y.Yu, Y.Wu, L.R.Lu, and Z.Y.Sheng (2002).
The significance of changes in high mobility group-1 protein mRNA expression in rats after thermal injury.
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12555809 X.Lv, D.D.Xu, D.P.Liu, L.Li, D.L.Hao, and C.C.Liang (2002).
High-mobility group protein 2 may be involved in the locus control region regulation of the beta-globin gene cluster.
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11297928 A.Hillisch, M.Lorenz, and S.Diekmann (2001).
Recent advances in FRET: distance determination in protein-DNA complexes.
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11353072 C.Hofr, N.Farrell, and V.Brabec (2001).
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11455562 J.L.Beck, M.L.Colgrave, S.F.Ralph, and M.M.Sheil (2001).
Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins.
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11246022 J.O.Thomas, and A.A.Travers (2001).
HMG1 and 2, and related 'architectural' DNA-binding proteins.
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Intramolecular DNA Coiling Mediated by a Metallo-Supramolecular Cylinder Support by the Leverhulme Trust (F/215/BC) and the EPSRC lifesciences interface network (GR/M91105) is gratefully acknowledged. Discussions with Julie MacPherson have been of great assistance during preparation of the manuscript.
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11294645 M.Stros (2001).
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PDB code: 1i11
11344319 R.Cerdan, D.Payet, J.C.Yang, A.A.Travers, and D.Neuhaus (2001).
HMG-D complexed to a bulge DNA: an NMR model.
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PDB code: 1e7j
11746919 R.Gupta, A.Kapur, J.L.Beck, and M.M.Sheil (2001).
Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes.
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Kinetic studies of the TATA-binding protein interaction with cisplatin-modified DNA.
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Recognition of distorted DNA structures by HMG domains.
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10710428 C.I.Webster, M.A.Cooper, L.C.Packman, D.H.Williams, and J.C.Gray (2000).
Kinetic analysis of high-mobility-group proteins HMG-1 and HMG-I/Y binding to cholesterol-tagged DNA on a supported lipid monolayer.
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Stopped-flow fluorescence studies of HMG-domain protein binding to cisplatin-modified DNA.
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Nonsequence-specific DNA recognition: a structural perspective.
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Conformational analysis of site-specific DNA cross-links of cisplatin-distamycin conjugates.
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DNA binding by single HMG box model proteins.
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DNA interactions of antitumor cisplatin analogs containing enantiomeric amine ligands.
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Mechanism for specificity by HMG-1 in enhanceosome assembly.
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DNA-interactions and nuclear localisation of the chromosomal HMG domain protein SSRP1 from maize.
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Structural studies of the high mobility group globular domain and basic tail of HMG-D bound to disulfide cross-linked DNA.
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10606643 M.Decoville, M.J.Giraud-Panis, C.Mosrin-Huaman, M.Leng, and D.Locker (2000).
HMG boxes of DSP1 protein interact with the rel homology domain of transcription factors.
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10891085 M.Kartalou, L.D.Samson, and J.M.Essigmann (2000).
Cisplatin adducts inhibit 1,N(6)-ethenoadenine repair by interacting with the human 3-methyladenine DNA glycosylase.
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Enhanced binding of the TATA-binding protein to TATA boxes containing flanking cisplatin 1,2-cross-links.
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DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
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PDB code: 1diz
11012880 T.Iida, Y.Makino, K.Okamoto, N.Yoshikawa, I.Makino, T.Nakamura, and H.Tanaka (2000).
Functional modulation of the mineralocorticoid receptor by cis-diamminedichloroplatinum (II).
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10590893 A.J.Windebank (1999).
Chemotherapeutic neuropathy.
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The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition.
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PDB code: 1qrv
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