PDBsum entry 5ivw

Transcription/DNA

PDB id: 5ivw

Contents

Protein chains

475 a.a.

665 a.a.

188 a.a.

62 a.a.

274 a.a.

193 a.a.

DNA/RNA

PDB id:

5ivw

Name:

Transcription/DNA

Title:

Human core tfiih bound to DNA within the pic

Structure:

Tfiih basal transcription factor complex helicase xpb subunit. Chain: v. Synonym: basic transcription factor 2 89 kda subunit, btf2 p89, DNA excision repair protein ercc-3, DNA repair protein complementing xp-b cells, tfiih basal transcription factor complex 89 kda subunit, tfiih p89, xeroderma pigmentosum group b-complementing protein. Tfiih basal transcription factor complex helicase xpd subunit.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Organism_taxid: 9606

Authors:

Y.He,C.Yan,J.Fang,C.Inouye,R.Tjian,I.Ivanov,E.Nogales

Key ref:

Y.He et al. (2016). Near-atomic resolution visualization of human transcription promoter opening. Nature, 533, 359-365. PubMed id: 27193682 DOI: 10.1038/nature17970

Date:

21-Mar-16 Release date: 18-May-16

Protein chain

P19447  (ERCC3_HUMAN) -  General transcription and DNA repair factor IIH helicase subunit XPB from Homo sapiens

Seq: 782 a.a.

Struc: 475 a.a.

Protein chain

P18074  (ERCC2_HUMAN) -  General transcription and DNA repair factor IIH helicase subunit XPD from Homo sapiens

Seq: 760 a.a.

Struc: 665 a.a.

Protein chain

Q13888  (TF2H2_HUMAN) -  General transcription factor IIH subunit 2 from Homo sapiens

Seq: 395 a.a.

Struc: 188 a.a.

Protein chain

Q6ZYL4  (TF2H5_HUMAN) -  General transcription factor IIH subunit 5 from Homo sapiens

Seq: 71 a.a.

Struc: 62 a.a.

Protein chain

Q92759  (TF2H4_HUMAN) -  General transcription factor IIH subunit 4 from Homo sapiens

Seq: 462 a.a.

Struc: 274 a.a.

Protein chain

Q13889  (TF2H3_HUMAN) -  General transcription factor IIH subunit 3 from Homo sapiens

Seq: 308 a.a.

Struc: 193 a.a.

DNA/RNA chains

A-T-T-G-C-C-G-A-A-G-A-C-G-A-A-A-A-A-A 19 bases

T-T-T-T-T-T-T-C-G-T-C-T-T-C-G-G-C-A-A-T 20 bases

Enzyme reactions

• Enzyme class 1: Chains 0, 1, 2, 3: E.C.?
• Enzyme class 2: Chains V, W: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature17970

Nature 533:359-365 (2016)

PubMed id: 27193682

Near-atomic resolution visualization of human transcription promoter opening.

Y.He, C.Yan, J.Fang, C.Inouye, R.Tjian, I.Ivanov, E.Nogales.

ABSTRACT

In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.