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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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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

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 ... F8N   [ 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.

All the 3 steps occur at the edge of the major groove region centered at SHL -6, in the structures 1P3F , 1P3O and 2F8N .

The remaining eighteen structures corresponding to sequence 5 display a variety of histone mutations and binding by different ligands: mutations in histones H3 and H4 (PDB id's 1P34 , 1P3A , 1P3B , 1P3F , 1P3G , 1P3I , 1P3K , 1P3L , 1P3M , 1P3O , 1P3P , 3C1B ), mutation in H2A to give H2A.Z (PDB id 1F66 ), presence of a linker joining the two DNA disks (PDB id 1S32 ), presence of groove binding ligands (PDB id's 1M18 , 1M19 , 1M1A ) and presence of an antigen bound to DNA (PDB id 1ZLA).

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