4B0A: PDB entry 4B0A

Name: PDB 4B0A: The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation
Published: 2013-07-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation. Determined by X-ray diffraction at 1.97 Å resolution. Released 3 Jul 2013.

Method: X-ray diffraction
Resolution: 1.97 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 1
Atoms: 2,189
Mol. weight: 31.02 kDa
Ligands: CA
Released: 3 Jul 2013

Explore 4B0A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4B0A contains 6 α-helices and 14 β-strands across 1 chain. 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	15-23	9
α-helix	28-35	8
β-strand	55	1	1
β-strand	166-175	10	2
α-helix	182-188	7
β-strand	189	1	1
β-strand	192-194	3	2
β-strand	202-206	5	2
β-strand	211-215	5	2
β-strand	220-226	7	2
α-helix	229-246	18
β-strand	253-265	13	2
β-strand	270	1	3
α-helix	272-278	7
β-strand	283-284	2	2
β-strand	293-296	4	2
β-strand	303-306	4	2
β-strand	311-317	7	2
α-helix	320-336	17
β-strand	338	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription initiation factor tfiid subunit 1, linker, tata-box-binding protein	A	protein	278	SACCHAROMYCES CEREVISIAE	P13393 (AlphaFold model), P46677 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4B0A_1 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, TATA-BOX-BINDING PROTEIN (chains A)
MGSSHHHHHHSSGLVPRGSHMGKTNLANEDEAYEAIFGGEFGSLEIGSYIGGDEARNSKD
YTEHLPDAVDFEDEDELADDDDDLPGGGSGGGSGGGSMSGIVPTLQNIVATVTLGCRLDL
KTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARI
IQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKI
VLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (CL, GOL) are not listed.

Primary citation

High-Resolution Structure of TBP with Taf1 Reveals Anchoring Patterns in Transcriptional Regulation. Anandapadamanaban, M., Andresen, C., Siponen, M. et al. Nat Struct Mol Biol (2013) 20:1008. DOI 10.1038/NSMB.2611 · PubMed

Other PDB entries of the same protein (UniProt P13393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1YTB 1.8 Å, Crystal structure of a yeast tbp/tata-box complex
1NH2 1.9 Å, Crystal structure of a yeast TFIIA/TBP/DNA complex
6E16 2.4 Å, Ternary structure of c-Myc-TBP-TAF1
1RM1 2.5 Å, Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex
1YTF 2.5 Å, Yeast tfiia/tbp/dna complex
1TBP 2.6 Å, Crystal structure of yeast tata-binding protein and model for interaction with DNA
7Z0O 2.8 Å, Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA
7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
7OHA 2.9 Å, nucleosome with TBP and TFIIA bound at SHL +2
1NGM 2.95 Å, Crystal structure of a yeast Brf1-TBP-DNA ternary complex
7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
7OH9 3.0 Å, Nucleosome with TBP and TFIIA bound at SHL -6

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