PDBsum entry 6j4z

Transcription/RNA/DNA

PDB id: 6j4z

Contents

Protein chains

1414 a.a.

1157 a.a.

263 a.a.

168 a.a.

213 a.a.

84 a.a.

171 a.a.

133 a.a.

111 a.a.

66 a.a.

113 a.a.

45 a.a.

102 a.a.

275 a.a.

97 a.a.

80 a.a.

103 a.a.

95 a.a.

DNA/RNA

Metals

_MG

_ZN ×9

PDB id:

6j4z

Name:

Transcription/RNA/DNA

Title:

RNA polymerase ii elongation complex bound with spt4/5 and foreign DNA, stalled at shl(-1) of the nucleosome

Structure:

DNA-directed RNA polymerase subunit. Chain: a. DNA-directed RNA polymerase subunit beta. Chain: b. RNA polymerase ii third largest subunit b44, part of central core. Chain: c. RNA polymerase ii subunit b32. Chain: d.

Source:

Komagataella phaffii (strain gs115 / atcc 20864). Yeast. Organism_taxid: 644223. Strain: gs115 / atcc 20864. Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1). Organism_taxid: 981350. Strain: atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner

Authors:

H.Ehara,T.Kujirai,Y.Fujino,M.Shirouzu,H.Kurumizaka,S.Sekine

Key ref:

H.Ehara et al. (2019). Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science, 363, 744-747. PubMed id: 30733384 DOI: 10.1126/science.aav8912

Date:

10-Jan-19 Release date: 20-Feb-19

Protein chain

C4R4Y0  (C4R4Y0_KOMPG) -  DNA-directed RNA polymerase subunit from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 1743 a.a.

Struc: 1414 a.a.

Protein chain

C4QZQ7  (C4QZQ7_KOMPG) -  DNA-directed RNA polymerase subunit beta from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 1227 a.a.

Struc: 1157 a.a.

Protein chain

C4R7L2  (C4R7L2_KOMPG) -  RNA polymerase II third largest subunit B44, part of central core from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 304 a.a.

Struc: 263 a.a.

Protein chain

C4R2U9  (C4R2U9_KOMPG) -  RNA polymerase II subunit B32 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 186 a.a.

Struc: 168 a.a.

Protein chain

C4R3P8  (C4R3P8_KOMPG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 214 a.a.

Struc: 213 a.a.

Protein chain

C4R1V1  (C4R1V1_KOMPG) -  RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 155 a.a.

Struc: 84 a.a.

Protein chain

C4R9A1  (C4R9A1_KOMPG) -  DNA-directed RNA polymerase subunit from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 171 a.a.

Struc: 171 a.a.

Protein chain

C4R273  (C4R273_KOMPG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 145 a.a.

Struc: 133 a.a.

Protein chain

F2QPE6  (F2QPE6_KOMPC) -  DNA-directed RNA polymerase subunit from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)

Seq: 115 a.a.

Struc: 111 a.a.

Protein chain

C4R009  (C4R009_KOMPG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 72 a.a.

Struc: 66 a.a.

Protein chain

C4R3Z5  (C4R3Z5_KOMPG) -  RNA polymerase II subunit B12.5 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 118 a.a.

Struc: 113 a.a.

Protein chain

F2QMI1  (F2QMI1_KOMPC) -  RNA polymerase subunit ABC10-alpha from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)

Seq: 72 a.a.

Struc: 45 a.a.

Protein chain

C4R0E6  (C4R0E6_KOMPG) -  Transcription elongation factor SPT4 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 114 a.a.

Struc: 102 a.a.

Protein chain

C4R370  (C4R370_KOMPG) -  Transcription elongation factor SPT5 from Komagataella phaffii (strain GS115 / ATCC 20864)

Seq: 908 a.a.

Struc: 275 a.a.*

Protein chains

P84243  (H33_HUMAN) -  Histone H3.3 from Homo sapiens

Seq: 136 a.a.

Struc: 97 a.a.

Protein chains

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 80 a.a.

Protein chains

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

Seq: 130 a.a.

Struc: 103 a.a.

Protein chains

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

Seq: 126 a.a.

Struc: 95 a.a.

* PDB and UniProt seqs differ at 57 residue positions (black crosses)

DNA/RNA chains

G-C-C-U-G-G-U-G-U-C-U-U-G-G-G-U 16 bases

A-T-C-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- 128 bases

T-C-T-C-G-T-G-C-C-T-G-G-T-G-T-C-T-T-T-A-A-T-C-C-C-C-T-T-G-G-C-G-G-T-T-A-A-A-A- 123 bases

G-G-G-G-A-T-T-A-C-A-C-C-C-A-A-G-A-C-A-C-C-A-G-G-C-A-C-G-A-G-A-C-A-G-A-A-A-A-A- 42 bases

G-T-T-T-T-T-T-T-C-T-G-T-C-T-C-G-T-G-C-C-T-G-G-T-G-T-C-T-T-G-G-G-T-G-T-A-A-T-C- 42 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1126/science.aav8912

Science 363:744-747 (2019)

PubMed id: 30733384

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.

H.Ehara, T.Kujirai, Y.Fujino, M.Shirouzu, H.Kurumizaka, S.I.Sekine.

ABSTRACT

RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.