Citations in PubMed

Primary Citation PubMed: 12079350 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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The structural basis for promoter -35 element recognition by the group IV sigma factors.

(2006) PLoS Biol 4

PubMed: 16903784 | PubMedCentral: PMC1540707 | DOI: 10.1371/journal.pbio.0040269

The Protein Data Bank accession number for the nucleosome structure in Figure S2 A is 1KX4.

Publication Year: 2006


Sequence-dependent DNA deformability studied using molecular dynamics simulations.

(2007) Nucleic Acids Res 35

PubMed: 17766249 | PubMedCentral: PMC2094071 | DOI: 10.1093/nar/gkm627

As a preliminary test, we evaluated the fitness of co-crystallized DNA sequences against histones ( 31 ) (PDB code: 1kx3, 1kx4 and 1kx5) by threading the DNA sequences on each of the three nucleosome ... ore structures.

Evaluation of fitness for nucleosome core structure DNA sequences were threaded on known nucleosome core structures (PDB codes: 1kx3, 1kx4 and 1kx5) ( 31 ), and the fitness of each of the three co-crystallized DNA sequences to each of the three structures was evaluated in the form of a Z-score that was calculated as the deviation of the energy of the target sequence from the energy distribution of random DNA sequences.

Publication Year: 2007


An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression.

(2011) BMC Struct Biol 11

PubMed: 21208404 | PubMedCentral: PMC3031206 | DOI: 10.1186/1472-6807-11-1

Crosscorrelation values for the successive bending angles, and the minor groove width, for the five structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 ... nd 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

Thus at SHL -1.5 in the structure 1F66 , the roll value is -68.1° with corresponding tilt, twist, shift, slide and rise values of -4.3°, 43.0°, 0.3 Å, 1.2 Å and 4.7 Å respectively, while the GG/CC steps in 1KX4 at SHL ±1.5 provide examples of distortion without stretching, but with positive slide values.

The trajectories for the dinucleotide step parameters, for the six structures, namely, 1KX4 , 2NZD , 2F8N , 1KX3 , 1P3I and 1KX5 , corresponding to sequences 1, 2, 3, 4, 5 and 6 respectively, are shown in figures S1-S6 of additional file 1 .

Figure S9 in additional file 1 shows the trajectories for the successive bending angles for the six representative structures, while Figure 5 (upper panel) shows the crosscorrelation values for the successive bending angles, for the five structures 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , with respect to the corresponding parameters for the structrure 1KX5 .

Sequences 1 and 2 had only one corresponding structure, namely 1KX4   [ 15 ] and 2NZD [ 31 ] respectively, sequences 3 and 6 had two corresponding structures, namely 1U35   [ 49 ] and 2F8N   [ 31 ], and 1KX5   [ 15 ] and 2PYO   [ 50 ] respectively, sequence 4 had three corresponding structures, namely 1AOI   [ 51 ], 1KX3   [ 15 ] and 2CV5   [ 27 ], while the remaining twenty structures ( 1EQZ   [ 52 ], 1F66   [ 53 ], 1M18 , 1M19 , 1M1A   [ 54 ], 1P34 , 1P3A , 1P3B , 1P3F , 1P3G , 1P3I , 1P3K , 1P3L , 1P3M , 1P3O , 1P3P   [ 55 ], 1S32   [ 56 ], 1ZLA   [ 57 ], 2NQB   [ 31 ], 3C1B   [ 58 ]) correspond to sequence 5.

Crosscorrelation values for the rotational parameters roll and twist, and the translational parameter slide, for the five structures with PDB ids 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

Figure 4 shows the crosscorrelation values for the parameters roll, twist and slide, for the five structures 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the parameters for the best resolved crystal structrure 1KX5 , corresponding to sequence 6.

Of these, only one step in the structure 1KX4 has an A-like Z p value of 1.3 Å, while the other nine steps have Z p values signifying an intermediate conformation.

This clearly indicates that the pattern of local bending is very distinct across different structures, despite very similar sequences for all the structures, except 1KX4 .

Crosscorrelation values for the angles between global helix axes fitted to backbone C 1 ' atoms of successive, non-overlapping tetranucleotide fragments, and the angles between global helix axes fitted to backbone C 1 ' atoms of successive, non-overlapping pentanucleotide fragments, for the five structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 and 1P3I , corresponding to sequences 1, 2, 3, 4 and 5, with respect to the corresponding parameters for the best resolved crystal structrure of the nucleosome with PDB id 1KX5 , corresponding to sequence 6.

All the structures corresponding to sequences 1 (PDB id 1KX4 ), 2 (PDB id 2NZD ), 4 (PDB id's 1AOI , 1KX3 and 2CV5 ) and 6 (PDB id's 1KX5 and 2PYO ), as well as one structure corresponding to sequence 3 (PDB id 2F8N ) and two structures corresponding to sequence 5 (PDB id's 1EQZ and 2NQB ) comprise of wild-type histones, though the histone sequence might vary at a few amino acid positions depending on the organism from which it was derived.

Autocorrelation values for the rotational parameters roll and twist, and the translational parameter slide, for the six structures with PDB id's 1KX4 , 2NZD , 2F8N , 1KX3 , 1P3I and 1KX5 , corresponding to sequences 1, 2, 3, 4, 5 and 6 respectively.

PDB id d/l local I max /I min I m a x + I m i d I m i n ROC (Å) 1KX4 0.707 (0.018) 5.9 (0.5) 11.1 (1.1) 41.9 (2.0) 2NZD 0.707 (0.020) 5.8 (0.5) 11.0 (1.0) 41.8 (2.0) 1U35 0.710 (0.017) 5.9 (0.5) 11.1 (1.1) 42.0 (1.9) 2F8N 0.714 (0.017) 5.9 (0.5) 11.1 (1.1) 41.9 (2.0) 1AOI 0.710 (0.019) 5.9 (0.5) 11.0 (1.0) 42.0 (2.0) 1KX3 0.707 (0.020) 5.9 (0.5) 11.0 (1.0) 41.7 (2.0) 2CV5 0.708 (0.017) 5.9 (0.5) 11.1 (1.0) 41.9 (1.9) 1EQZ 0.712 (0.018) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1F66 0.708 (0.016) 5.8 (0.5) 11.0 (1.0) 41.9 (2.1) 1M18 0.713 (0.017) 5.9 (0.5) 11.1 (1.0) 42.2 (2.0) 1M19 0.716 (0.017) 6.0 (0.5) 11.2 (1.1) 42.0 (1.9) 1M1A 0.712 (0.017) 5.9 (0.5) 11.1 (1.0) 42.0 (1.8) 1P34 0.708 (0.019) 5.9 (0.5) 11.1 (1.1) 42.0 (2.1) 1P3A 0.708 (0.019) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3B 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1P3F 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 41.8 (2.0) 1P3G 0.709 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3I 0.708 (0.019) 5.9 (0.5) 11.1 (1.0) 41.9 (2.0) 1P3K 0.705 (0.020) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3L 0.710 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3M 0.711 (0.020) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1P3O 0.708 (0.020) 5.9 (0.5) 11.0 (1.0) 41.9 (2.0) 1P3P 0.709 (0.019) 5.9 (0.5) 11.1 (1.0) 41.9 (2.0) 1S32 0.709 (0.019) 5.9 (0.4) 11.0 (0.9) 41.9 (1.9) 1ZLA 0.708 (0.019) 5.9 (0.5) 11.0 (1.0) 41.8 (2.0) 2NQB 0.708 (0.020) 5.8 (0.5) 11.0 (1.1) 41.9 (2.1) 3C1B 0.706 (0.019) 5.9 (0.5) 11.1 (1.0) 42.0 (2.0) 1KX5 0.714 (0.018) 6.0 (0.6) 11.2 (1.1) 41.9 (2.0) 2PYO 0.712 (0.019) 5.9 (0.6) 11.2 (1.1) 41.9 (2.1) Discussion Nucleosomal DNA is B-like at the dinucleotide step level An analysis of the twenty-nine nucleosome X-ray crystal structures of better than 3 Å resolution reveals significant dinucleotide level structural variability in nucleosomal DNA, despite limited variation in sequence, with only six unique sequences, of which only one differs significantly from the other five.

Publication Year: 2011


Statistical investigation of position-specific deformation pattern of nucleosome DNA based on multiple conformational properties.

(2011) Bioinformation 7

PubMed: 22125381 | PubMedCentral: PMC3218313 | DOI: null

Methodology Structural data of NCPs The experimental database is constructed by collecting 6870 base pair steps from 48 nucleosome crystal structures in the Protein Data Bank (PDB), including 1AOI, 1E... Z, 1F66, 1ID3, 1KX5, 1KX4, 1KX3, 1M1A, 1M19, 1M18, 1P3P, 1P3O, 1P3M, 1P3L, 1P3K, 1P3I, 1P3G, 1P3F, 1P3B, 1P3A, 1P34, 1S32, 2CV5, 1U35, 1ZLA, 2F8N, 2FJ7, 2NZD, 2NQB, 2PYO, 3B6G, 3B6F, 3C1C, 3C1B, 3KUY, 3LJA, 3KWQ, 3LEL, 3AFA, 3A6N, 3MGS, 3MGR, 3MGQ, 3MGP, 3KXB, 3MVD, 3LZ0 and 3LZ1.

Publication Year: 2011