PDBsum entry 5b24

Structural protein/DNA

PDB id: 5b24

Contents

Protein chains

97 a.a.

78 a.a.

108 a.a.

93 a.a.

84 a.a.

DNA/RNA

PDB id:

5b24

Name:

Structural protein/DNA

Title:

The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer

Structure:

Histone h3.1. Chain: a, e. Synonym: histone h3/a,histone h3/b,histone h3/c,histone h3/d,histone h3/f,histone h3/h,histone h3/i,histone h3/j,histone h3/k,histone h3/l. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hist1h3a, h3fa, hist1h3b, h3fl, hist1h3c, h3fc, hist1h3d, h3fb, hist1h3e, h3fd, hist1h3f, h3fi, hist1h3g, h3fh, hist1h3h, h3fk, hist1h3i, h3ff, hist1h3j, h3fj. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g,

Resolution:

3.60Å R-factor: 0.207 R-free: 0.250

Authors:

N.Horikoshi,H.Tachiwana,W.Kagawa,A.Osakabe,H.Kurumizaka

Key ref:

N.Horikoshi et al. (2016). Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer. Biochem Biophys Res Commun, 471, 117-122. PubMed id: 26837048 DOI: 10.1016/j.bbrc.2016.01.170

Date:

31-Dec-15 Release date: 02-Mar-16

Protein chains

P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens

Seq: 136 a.a.

Struc: 97 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens

Seq: 130 a.a.

Struc: 108 a.a.

Protein chains

P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J from Homo sapiens

Seq: 126 a.a.

Struc: 93 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 84 a.a.

DNA/RNA chains

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 145 bases

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 145 bases

DOI no: 10.1016/j.bbrc.2016.01.170

Biochem Biophys Res Commun 471:117-122 (2016)

PubMed id: 26837048

Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

N.Horikoshi, H.Tachiwana, W.Kagawa, A.Osakabe, S.Matsumoto, S.Iwai, K.Sugasawa, H.Kurumizaka.

ABSTRACT

The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.