PDBsum entry 8kd7

Transcription

PDB id: 8kd7

Contents

Protein chains

385 a.a.

536 a.a.

188 a.a.

302 a.a.

61 a.a.

69 a.a.

104 a.a.

79 a.a.

107 a.a.

92 a.a.

98 a.a.

DNA/RNA

PDB id:

8kd7

Name:

Transcription

Title:

Rpd3s in complex with nucleosome with h3k36mla modification and 167bp DNA

Structure:

Histone deacetylase rpd3. Chain: a. Engineered: yes. Transcriptional regulatory protein sin3. Chain: b. Engineered: yes. Chromatin modification-related protein eaf3. Chain: d, f. Synonym: esa1-associated factor 3.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rpd3. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Gene: sin3, cpe1, gam2, rpd1, sdi1, sds16, ume4, yol004w. Gene: eaf3. Gene: rco1.

Authors:

S.Dong,H.Li,M.Wang,N.Rasheed,B.Zou,X.Gao,J.Guan,W.Li,J.Zhang,C.Wang, N.Zhou,X.Shi,M.Li,M.Zhou,J.Huang,H.Li,Y.Zhang,K.H.Wong,X.Chang, W.C.H.Chao,J.He

Key ref:

S.Dong et al. Structural basis of nucleosome deacetylation and DNA tightening by rpd3s histone deacetylase complex. To be published, . PubMed id: 37666978

Date:

09-Aug-23 Release date: 13-Sep-23

Protein chain

P32561  (RPD3_YEAST) -  Histone deacetylase RPD3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 433 a.a.

Struc: 385 a.a.

Protein chain

P22579  (SIN3_YEAST) -  Transcriptional regulatory protein SIN3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1536 a.a.

Struc: 536 a.a.

Protein chain

Q12432  (EAF3_YEAST) -  Chromatin modification-related protein EAF3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 401 a.a.

Struc: 188 a.a.*

Protein chain

Q04779  (RCO1_YEAST) -  Transcriptional regulatory protein RCO1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 684 a.a.

Struc: 302 a.a.*

Protein chain

Q12432  (EAF3_YEAST) -  Chromatin modification-related protein EAF3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 401 a.a.

Struc: 61 a.a.

Protein chain

Q04779  (RCO1_YEAST) -  Transcriptional regulatory protein RCO1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 684 a.a.

Struc: 69 a.a.*

Protein chain

P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis

Seq: 136 a.a.

Struc: 104 a.a.*

Protein chains

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 79 a.a.

Protein chains

P06897  (H2A1_XENLA) -  Histone H2A type 1 from Xenopus laevis

Seq: 130 a.a.

Struc: 107 a.a.*

Protein chains

P02281  (H2B11_XENLA) -  Histone H2B 1.1 from Xenopus laevis

Seq: 126 a.a.

Struc: 92 a.a.*

Protein chain

P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis

Seq: 136 a.a.

Struc: 98 a.a.*

* PDB and UniProt seqs differ at 68 residue positions (black crosses)

DNA/RNA chains

T-C-T-A-G-A-A-C-A-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A- 153 bases

T-G-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G- 152 bases

Enzyme reactions

• Enzyme class: Chain A: E.C.3.5.1.98 - histone deacetylase.
• Reaction: N₆-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site