Primary Citation PubMed: 10385126
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Variation in structural location and amino acid conservation of functional sites in protein domain families.
(2005) BMC Bioinformatics 6
PubMed: 16122386 | PubMedCentral: PMC1215474 | DOI: 10.1186/1471-2105-6-210
In contrast, a phenylalanine establishes the contact in figure 3b (pdb id: 1ckt [ 28 ]) and the serine residue corresponding to the structure shown in 3a is pointing away from the DNA helix.
Publication Year: 2005
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.
(2008) Nucleic Acids Res 36
PubMed: 18515834 | PubMedCentral: PMC2475640 | DOI: 10.1093/nar/gkn353
Left, HMG box A from mammalian HMGB1 ( 37 , 38 , 41 ), PDB code 1CKT, which is highly similar to the corresponding box from HMGB2.
Publication Year: 2008
Insights into protein-DNA interactions through structure network analysis.
(2008) PLoS Comput Biol 4
PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170
Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).
Structural basis for the sequence-dependent effects of platinum-DNA adducts.
(2009) Nucleic Acids Res 37
PubMed: 19255091 | PubMedCentral: PMC2677858 | DOI: 10.1093/nar/gkp029
For the simulations of HMGB1a-Pt–DNA complex, we used the crystal structure of rat HMGB1a bound to CP-DNA in the T GG A sequence context as the starting structure for the CP-T GG A simulations... [PDB ID 1ckt ( 21 )].
Publication Year: 2009
Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.
PubMed: 19304746 | PubMedCentral: PMC2691818 | DOI: 10.1093/nar/gkp157
Structural comparison of selected HMG boxes PDB Protein RMSD (Å) Method 2HDZ UBF box 5 1.35 X-Ray 1J3C HMGB2 box B 1.40 NMR 1QRV HMGD/DNA 1.49 X-Ray 2LEF LEF1/DNA 1.50 NMR 1CKT HMGB1 box A/DNA... 1.87 X-Ray 1J3X HMGB2 box A 2.04 NMR 1HMF HMGB1 box B 2.23 NMR 2YUL SOX17 2.28 NMR 2YQI HMGB3 box B 2.33 NMR 2EZQ HMGB3 box A 2.36 NMR 1V63 UBF box 6 2.38 NMR 1AAB HMGB1 box A 2.53 NMR 1GTO SOX2/DNA 2.93 X-Ray 1V64 UBF box 3 3.10 NMR 1K99 UBF box 1 3.13 NMR 1HRY SRY/DNA 3.73 NMR 1WGF UBF box 4 5.42 NMR Despite the differences in the tertiary structural features of box B of h-mtTFA compared to other HMG boxes, the surface electrostatic features of the HMG boxes are similar.
( A ) Structural superposition of box B of h-mtTFA (3fgh; red) overlaid with HMGD (1qrv; yellow), UBF box 5 (2hdz; green), LEF1 (2lef; purple), HMGB1 box A (1ckt; cyan) and Sox2 (1gt0; black).
Overall RMSD values were calculated between each amino acid of the structures of HMGD [PDB ID 1qrv ( 36 )], SOX2 HMG box A (PDB ID 1gt0, Remenyi, A., Scholer, H.R., Wilmanns, M. unpublished), HMGB1 box A [PDB ID 1ckt ( 37 )], LEF1 [PDB ID 2lef ( 38 )] and UBF5 [PDB ID 2hdz; Rong, H., Teng, M.K., and Niu, L., unpublished data)] and the X-ray crystal structure of h-mtTFA box B using the program COOT ( 33 ).
The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.
(2011) Nat Struct Mol Biol 18
PubMed: 22037171 | PubMedCentral: PMC3210390 | DOI: 10.1038/nsmb.2159
Structures correspond to the following accession numbers, and RMSD values, relative to HMG-box A of Tfam, are provided in parentheses: HMG-box B of Tfam without DNA, 3fgh 19 (0.974); Hmgb1 box A, 1ckt... 27 (1.101); Lef1, 2lef 28 (1.162); Sox2, 1gt0 29 (1.152); Hmgd, 1qrv 30 (1.127).
Publication Year: 2011
A nuclear factor of high mobility group box protein in Toxoplasma gondii.
(2014) PLoS One 9
PubMed: 25369210 | PubMedCentral: PMC4219823 | DOI: 10.1371/journal.pone.0111993
TgHMGB1a is a typical one HMG box protein and concentrated in nuclear in intracellular tachyzoites but translocated into cytoplasm while it's in extracellular The ternary structure of full length TgHM... B1a ( Figure 2 A ) was modeled using the structure template of 1ckt A chain.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
Following PDB structures were used: SRY—1j46 [ 36 ], HMGB1a-1ckt [ 41 ], MAEL HMG—2cto [ 45 ].
Determined structures of candidate HMG-box proteins (SRY: 1j46—sequence specific binding; HMGB1a: 1ckt—structure specific binding; MAEL: 2cto—unknown binding) were visualized and structures aligned in PyMOL.
Publication Year: 2015
This DNA and the full protein coordinates of HMGB1 box A (Pro8–Tyr77 in Fig. 1 ▸ ; Ohndorf et al. , 1999 ▸ ; PDB entry 1ckt ) were used as a search model for molecular replacem... nt.
Superimposition of box A from this structure (cyan) with ( a ) box A from cisplatin-modified DNA (PDB entry 1ckt ; gray; Ohndorf et al. , 1999 ▸ ), ( b ) box A from the solution structure of the oxidized form (PDB entry 2rtu ; gray; Wang et al. , 2013 ▸ ) and ( c ) the C22S mutant box A free reduced form (PDB entry 1aab ; gray; Hardman et al. , 1995 ▸ ).
The roll and twist angles for box A in this structure were obtained with 3 DNA , and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al. , 1999 ▸ ), 2gzk (box B; Stott et al. , 2006 ▸ ), 1qrv (HMGD; Murphy et al. , 1999 ▸ ), 1j5n (NHP6A; Masse et al. , 2002 ▸ ) and 3tmm (TFAM; Ngo et al. , 2011 ▸ ) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2).
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