1NH2: Yeast TFIIA/TBP/DNA complex

Crystal structure of a yeast TFIIA/TBP/DNA complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Oct 2003.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 4,204
Mol. weight: 58.53 kDa
Released: 21 Oct 2003

Explore 1NH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NH2 contains 11 α-helices and 20 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66-75	10	1
α-helix	82-88	7
β-strand	89	1	2
β-strand	92-94	3	1
β-strand	102-107	6	1
β-strand	110-115	6	1
β-strand	120-126	7	1
α-helix	129-146	18
β-strand	153-165	13	1
β-strand	170	1	3
α-helix	172-178	7
β-strand	183-184	2	1
β-strand	193-197	5	1
β-strand	202-206	5	1
β-strand	211-217	7	1
α-helix	220-236	17
β-strand	238	1	3

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-20	17
α-helix	22-27	6
α-helix	32-47	16

Chain C: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	230	1	2
β-strand	243-254	12	1
β-strand	257-269	13	1
β-strand	272-284	13	1

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-28	15
α-helix	34-54	21
β-strand	59-72	14	1
β-strand	75-88	14	1
β-strand	104-117	14	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-D(TPGPTPAP(5IU)PGPTPAPTPAP(5IU)PAPAPAPAPC)-3'	E	DNA	16
5'-d(gptptptptpaptpaptpapcpaptpapcpa)-3'	F	DNA	16
Transcription initiation factor TFIID	A	protein	180	Saccharomyces cerevisiae	P13393 (AlphaFold model)
Transcription initiation factor IIA large chain	B	protein	53	Saccharomyces cerevisiae	P32773 (AlphaFold model)
Transcription initiation factor IIA large chain	C	protein	79	Saccharomyces cerevisiae	P32773 (AlphaFold model)
Transcription initiation factor IIA small chain	D	protein	121	Saccharomyces cerevisiae	P32774 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>1NH2_1 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)P*AP*AP*AP*AP*C)-3' (chains E)
TGTAUGTATAUAAAAC

Sequence of entity 2 (F), FASTA

>1NH2_2 5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3' (chains F)
GTTTTATATACATACA

Sequence of entity 3 (A), FASTA

>1NH2_3 Transcription initiation factor TFIID (chains A)
SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK
MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG
TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Sequence of entity 4 (B), FASTA

>1NH2_4 Transcription initiation factor IIA large chain (chains B)
SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTF

Sequence of entity 5 (C), FASTA

>1NH2_5 Transcription initiation factor IIA large chain (chains C)
GSSALLDTDEVGSELDDSDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVV
TINRNDYTFQKAQVEAEWV

Sequence of entity 6 (D), FASTA

>1NH2_6 Transcription initiation factor IIA small chain (chains D)
AVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLT
VKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKS
E

Primary citation

Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. Bleichenbacher, M., Tan, S., Richmond, T.J. J Mol Biol (2003) 332:783-793. DOI 10.1016/S0022-2836(03)00887-8 · 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
4B0A 1.97 Å, The high-resolution structure of yTBP-yTAF1 identifies conserved and competing…
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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