Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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.

Publication Year: 2013


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

PubMedCentral: PMC4465831

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).

Publication Year: 2015