3DOM: PDB entry 3DOM

Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2. Determined by X-ray diffraction at 2.6 Å resolution. Released 19 Aug 2008.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 2,323
Mol. weight: 41.52 kDa
Released: 19 Aug 2008

Explore 3DOM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DOM contains 15 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	440-448	9
β-strand	452-460	9	1
α-helix	465-478	14
β-strand	481-485	5	1
α-helix	486-488	3
β-strand	490-494	5	1
α-helix	495-497	3
α-helix	498-508	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	1
α-helix	14-27	14
β-strand	31-36	6	1
β-strand	39-42	4	1
α-helix	44-46	3
α-helix	47-57	11

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	435-448	14
β-strand	452-459	8	2
α-helix	465-477	13
β-strand	481-485	5	2
β-strand	490-494	5	2
α-helix	495-497	3
α-helix	498-506	9

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	2
α-helix	14-24	11
β-strand	31-36	6	2
β-strand	39-42	4	2
α-helix	44-46	3
α-helix	47-60	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase II transcription factor B subunit 2	A, C	protein	108	Saccharomyces cerevisiae	Q02939 (AlphaFold model)
RNA polymerase II transcription factor B subunit 5	B, D	protein	71	Saccharomyces cerevisiae	Q3E7C1 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3DOM_1 RNA polymerase II transcription factor B subunit 2 (chains A, C)
GPHMASAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETS
QEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Sequence of entity 2 (B, D), FASTA

>3DOM_2 RNA polymerase II transcription factor B subunit 5 (chains B, D)
ARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKN
IYNPMDEEENQ

Primary citation

Structural basis for group A trichothiodystrophy. Kainov, D.E., Vitorino, M., Cavarelli, J. et al. Nat Struct Mol Biol (2008) 15:980-984. PubMed

Other PDB entries of the same protein (UniProt Q02939 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DGP 1.8 Å, Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2
7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
7ML4 3.1 Å, RNA polymerase II initially transcribing complex (ITC)
7ZS9 3.1 Å, Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome…
7O4I 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with initial transcription…
7O75 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
7O4L 3.4 Å, Yeast TFIIH in the expanded state within the pre-initiation complex
7O72 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
7O73 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed distorted…

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