Primary Citation PubMed: 14559893
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Evolutionary conservation of DNA-contact residues in DNA-binding domains.
(2008) BMC Bioinformatics 9 Suppl 6
PubMed: 18541056 | PubMedCentral: PMC2423444 | DOI: 10.1186/1471-2105-9-S6-S3
The alignment with the maximum number of identical aligned pairs is chosen, and as a result the alignment between 1B8I-C and 1O4X-C is the one chosen (Figure 4C ).
According to z-scores, these 13 domains can be roughly divided into two groups, including the Ubx-like homeodomain colored in blue (e.g. PDB entry 9ANT-A (12.77), 1AHD-P (12.19), and 1SAN (11.96)) and the Oct-1 POU homeodomain colored in red (e.g. PDB entry 1E3O-C1 (6.40), 1GT0-C1 (6.38), and 1O4X-A1 (4.40)).
The z-scores indicated that the contact residues between 1PUF-A and 1B8I-A are more conserved than the ones between 1O4X-A1 and 1B8I-A on contact residues interacting to the bases of the core binding site in the DNA.
(C) Alignments of bound DNA sequences of the complexes 1B8I and 1O4X .
Then we adjust the alignment of the other DNA strand pairs (i.e. 1B8I-D and 1O4X-D ) according to this best alignment ( 1B8I-C and 1O4X-C ).
With respect to 1B8I-A , 1PUF-A and 1O4X-A1 are different not only in the DNA sequences they bind to but also in their DNA-binding sites.
The 1PUF-A and 1O4X-A1 (Oct-1 POU homeodomains from Homo sapiens [ 23 ]) are the members of the 1B8I-A representative domain.
1B8I-A binds two DNA sequences (i.e. PDB entry 1B8I-C and 1B8I-D ) and 1O4X-A1 binds another two DNA sequences (PDB entry 1O4X-C and 1O4X-D ).
Figures 4B and 4C show that the number of identical nucleotides between 1B8I-C and 1PUF-E (10) as well as 1B8I-D and 1PUF-D (10) is much higher than those of 1B8I-C and 1O4X-C (6) as well as 1B8I-D and 1O4X-D (5) for whole DNA sequences.
(A) The z-score values and the bound DNA sequences of the complex 1B8I (PDB entry 1B8I-C and 1B8I-D ), 1PUF (PDB entry 1PUF-D and 1PUF-E ), and 1O4X (PDB entry 1O4X-C and 1O4X-D ).
The z -scores are 11.92 ( 1PUF-A ) and 4.4 ( 1O4X-A1 ) when 1B8I-A was used as the query (Figure 4A ).
First we generated four pairing alignments: 1B8I-C and 1O4X-C ; 1B8I-C and 1O4X-D ; 1B8I-D and 1O4X-C ; and 1B8I-D and 1O4X-D .
At the same time, 11 identical contact nucleotides are obtained from the alignments of 1B8I-C and 1PUF-E as well as 1B8I-D and 1PUF-D ; but two identical contact nucleotides are yielded from the alignments of 1B8I-C and 1O4X-C as well as 1B8I-D and 1O4X-D (the contact nucleotides are the nucleotides that interact with contact residues of protein).
Publication Year: 2008
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements.
(2012) Nucleic Acids Res 40
PubMed: 22344693 | PubMedCentral: PMC3367189 | DOI: 10.1093/nar/gks153
Sox HMGs were subsequently superimposed onto the Sox2 HMG/Oct1 POU complex bound to a canonical element (pdb-id 1O4X).
Publication Year: 2012
On the need for mechanistic models in computational genomics and metagenomics.
(2013) Genome Biol Evol 5
PubMed: 24115604 | PubMedCentral: PMC3814209 | DOI: 10.1093/gbe/evt151
The image is generated from PDB file 1O4X.
Publication Year: 2013
Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis.
(2013) Comput Math Methods Med 2013
PubMed: 24324527 | PubMedCentral: PMC3845252 | DOI: 10.1155/2013/854710
Experimental Data Two POU/HMG/DNA ternary complexes, 1GT0 and 1O4X, are downloaded from the Protein Data Bank (PDB) [ 18 ] for analysis.
OCT1 is a determinant of synbindin-related ERK signalling with independent prognostic significance in gastric cancer.
(2015) Gut 64
PubMed: 24717932 | PubMedCentral: PMC4283676 | DOI: 10.1136/gutjnl-2013-306584
To identify the exact binding site of OCT1 on synbindin promoter, we developed a sequence scanning approach using the 3DTF method 25 based on the crystallographic data on the OCT1 protein–DNA ... omplex (pdb entry: 1O4X).
Publication Year: 2015
PubMed ID is not available.
Published in 2015
These were built based on the structure of the OCT1-SOX2- HOXB1 complex (pdbid 1O4X) [ 15 ] and the OCT4-OCT4-DNA homodimer complex [ 20 ] (see S1 Text for details).
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