1NVP: Human tfiia/tbp/dna complex

Human tfiia/tbp/dna complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 21 Oct 2003.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,858
Mol. weight: 58.37 kDa
Released: 21 Oct 2003

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

Secondary structure: helices and β-sheets

1NVP contains 10 α-helices and 18 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	163	1
β-strand	164-173	10	1
α-helix	180-186	7
β-strand	190-193	4	1
β-strand	197-205	9	1
β-strand	208-213	6	1
β-strand	218-222	5	1
α-helix	227-243	17
β-strand	251-263	13	1
β-strand	268	1	2
α-helix	270-276	7
β-strand	281-282	2	1
β-strand	291-295	5	1
β-strand	300-304	5	1
β-strand	309-315	7	1
α-helix	318-333	16
β-strand	336	1	2

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-32	23
α-helix	36-50	15

Chain C: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	334-345	12	1
β-strand	348-360	13	1
β-strand	363-375	13	1

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	10-24	15
α-helix	30-50	21
β-strand	55-68	14	1
β-strand	71-82	12	1
β-strand	87-98	12	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(gpgpgpgpgpgpgpcptpaptpapapapapgp*g)-3'	E	DNA	17
5'-d(cpcptptptptpaptpapgpcpcpcpcpcpcp*c)-3'	F	DNA	17
TATA box binding protein	A	protein	181	Homo sapiens	P20226 (AlphaFold model)
Transcription initiation factor IIA alpha chain	B	protein	57	Homo sapiens	P52655 (AlphaFold model)
Transcription initiation factor IIA beta chain	C	protein	76	Homo sapiens	P52655 (AlphaFold model)
Transcription initiation factor IIA gamma chain	D	protein	108	Homo sapiens	P52657 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>1NVP_1 5'-D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3' (chains E)
GGGGGGGCTATAAAAGG

Sequence of entity 2 (F), FASTA

>1NVP_2 5'-D(*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*CP*CP*CP*C)-3' (chains F)
CCTTTTATAGCCCCCCC

Sequence of entity 3 (A), FASTA

>1NVP_3 TATA box binding protein (chains A)
SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGK
MVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQ
QFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKT
T

Sequence of entity 4 (B), FASTA

>1NVP_4 Transcription initiation factor IIA alpha chain (chains B)
ANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAVDG

Sequence of entity 5 (C), FASTA

>1NVP_5 Transcription initiation factor IIA beta chain (chains C)
GSGAEDGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNL
NGRDYIFSKAIGDAEW

Sequence of entity 6 (D), FASTA

>1NVP_6 Transcription initiation factor IIA gamma chain (chains D)
AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFRGS
LNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE

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 P20226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CDW 1.9 Å, Human tbp core domain complexed with DNA
4ROC 1.9 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter
4ROE 2.2 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter
7NVU 2.5 Å, RNA polymerase II core pre-initiation complex with open promoter DNA
1JFI 2.62 Å, Crystal Structure of the NC2-TBP-DNA Ternary Complex
1C9B 2.65 Å, Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an…
4ROD 2.7 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter
5N9G 2.7 Å, TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-
7NVS 2.8 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal…
1TGH 2.9 Å, Tata binding protein (tbp)/dna complex
7NVT 2.9 Å, RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
8S52 2.9 Å, RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt

Browse structure collections

About this viewer

MolViewer shows 1NVP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.