1RM1: Yeast TFIIA/TBP/TATA-box DNA Complex

Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Jul 2005.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 4,200
Mol. weight: 83.78 kDa
Released: 26 Jul 2005

Explore 1RM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RM1 contains 11 α-helices and 20 β-strands across 3 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	101-107	7	1
β-strand	110-116	7	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	183-186	4	1
β-strand	190-197	8	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, 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	75-86	12	1
β-strand	106-117	12	1

Chain C: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-28	25
α-helix	32-49	18
α-helix	57-60	4
β-strand	230	1	2
β-strand	243-254	12	1
β-strand	257-268	12	1
β-strand	273-284	12	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(aptpcpgpaptpcpgpaptpaptpapapapapcpg)-3'	D	DNA	18
5'-d(pcpgptptptptpaptpaptpcpgpaptpcpgpapt)-3'	E	DNA	18
TATA-box binding protein	A	protein	240	Saccharomyces cerevisiae	P13393 (AlphaFold model)
Transcription initiation factor IIA small chain	B	protein	122	Saccharomyces cerevisiae	P32774 (AlphaFold model)
Transcription initiation factor IIA large chain	C	protein	286	Saccharomyces cerevisiae	P32773 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>1RM1_1 5'-D(*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*AP*TP*AP*AP*AP*AP*CP*G)-3' (chains D)
ATCGATCGATATAAAACG

Sequence of entity 2 (E), FASTA

>1RM1_2 5'-D(P*CP*GP*TP*TP*TP*TP*AP*TP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3' (chains E)
CGTTTTATATCGATCGAT

Sequence of entity 3 (A), FASTA

>1RM1_3 TATA-box binding protein (chains A)
MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSAT
SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK
MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG
TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Sequence of entity 4 (B), FASTA

>1RM1_4 Transcription initiation factor IIA small chain (chains B)
MAVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKL
TVKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKK
SE

Sequence of entity 5 (C), FASTA

>1RM1_5 Transcription initiation factor IIA large chain (chains C)
MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQF
NEGNINGVQNDLNFNLATPGVNSSEFNIKEENTGNEGLILPNINSNNNIPHSGETNINTN
TVEATNNSGATLNTNTSGNTNADVTSQPKIEVKPEIELTINNANITTVENIDDESEKKDD
EEKEEDVEKTRKEKEQIEQVKLQAKKEKRSALLDTDEVGSELDDSDDDYLISEGEEDGPD
ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV

Primary citation

High Resolution Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex. Jin, X., Gewirth, D.T., Geiger, J.H. To be published.

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
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
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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