1NGM: Yeast Brf1-TBP-DNA ternary complex

Crystal structure of a yeast Brf1-TBP-DNA ternary complex. Determined by X-ray diffraction at 2.95 Å resolution. Released 25 Mar 2003.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Saccharomyces cerevisiae
Chains: 16
Atoms: 10,800
Mol. weight: 160.4 kDa
Released: 25 Mar 2003

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

Secondary structure: helices and β-sheets

1NGM contains 42 α-helices and 52 β-strands across 8 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	69-75	7	1
α-helix	82-86	5
β-strand	93-94	2	2
β-strand	102-103	2	2
β-strand	115	1	2
β-strand	122-126	5	1
α-helix	130-135	6
α-helix	139-146	8
β-strand	153-156	4	1
β-strand	160-161	2	1
β-strand	163-165	3	3
α-helix	175-178	4
β-strand	183-184	2	3
β-strand	193-196	4	3
β-strand	203-206	4	3
β-strand	211-213	3	3
α-helix	220-236	17

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	442-444	3
α-helix	448-452	5
α-helix	470-472	3
α-helix	477-490	14
α-helix	494-500	7

Chain E: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66-75	10	4
α-helix	82-86	5
β-strand	89	1	5
β-strand	92-94	3	4
β-strand	101-104	4	4
β-strand	112-116	5	4
β-strand	120-126	7	4
α-helix	129-146	18
β-strand	153-165	13	4
α-helix	172-177	6
β-strand	183-184	2	4
β-strand	192-196	5	4
β-strand	203-207	5	4
β-strand	211-217	7	4
α-helix	220-236	17

Chain F: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	439-440	2
α-helix	442-444	3
α-helix	448-452	5
α-helix	463-465	3
α-helix	468-471	4
β-strand	474	1	5
α-helix	477-490	14
α-helix	492-504	13

Chain I: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66-75	10	6
α-helix	82-88	7
β-strand	92-95	4	6
β-strand	99-107	9	6
β-strand	110-116	7	6
β-strand	120-126	7	6
α-helix	129-146	18
β-strand	153-165	13	6
β-strand	170	1	7
α-helix	172-178	7
β-strand	183-184	2	6
β-strand	193-196	4	6
β-strand	203-206	4	6
β-strand	211-217	7	6
α-helix	220-230	11
α-helix	232-235	4
β-strand	238	1	7

Chain J: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	462-464	3
α-helix	468-471	4
α-helix	477-490	14
α-helix	492-500	9

Chain M: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66-75	10	8
α-helix	82-86	5
β-strand	89	1	9
β-strand	94	1	8
β-strand	101-104	4	8
β-strand	107	1	10
β-strand	110	1	10
β-strand	112-116	5	8
β-strand	120-126	7	8
α-helix	129-146	18
β-strand	153-165	13	8
β-strand	170	1	11
α-helix	172-178	7
β-strand	184-186	3	12
β-strand	190-194	5	12
β-strand	204	1	8
β-strand	211-214	4	8
α-helix	222-235	14
β-strand	238	1	11

Chain N: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	463-465	3
α-helix	468-470	3
β-strand	474	1	9
α-helix	478-490	13
α-helix	492-495	4
α-helix	501-504	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(cptpaptpapapapapapapaptpgptptptptptp*t)-3'	C, G, K, O	DNA	19
5'-d(apapapapapapcpaptptptptptptptpaptpap*g)-3'	D, H, L, P	DNA	19
Transcription initiation factor TFIID	A, E, I, M	protein	180	Saccharomyces cerevisiae	P13393 (AlphaFold model)
Transcription factor IIIB BRF1 subunit	B, F, J, N	protein	72	Saccharomyces cerevisiae	P29056 (AlphaFold model)

Sequence of entity 1 (C, G, K, O), FASTA

>1NGM_1 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' (chains C, G, K, O)
CTATAAAAAAATGTTTTTT

Sequence of entity 2 (D, H, L, P), FASTA

>1NGM_2 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' (chains D, H, L, P)
AAAAAACATTTTTTTATAG

Sequence of entity 3 (A, E, I, M), FASTA

>1NGM_3 Transcription initiation factor TFIID (chains A, E, I, M)
SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK
MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG
TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Sequence of entity 4 (B, F, J, N), FASTA

>1NGM_4 Transcription factor IIIB BRF1 subunit (chains B, F, J, N)
GSYCPRNLHLLPTTDTYLSKVSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADF
LLEQESKRLKQE

Primary citation

Crystal structure of a transcription factor IIIB core interface ternary complex. Juo, Z.S., Kassavetis, G.A., Wang, J. et al. Nature (2003) 422:534-539. DOI 10.1038/nature01534 · 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
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
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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