1CDW: Human tbp core domain

Human tbp core domain complexed with DNA. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Dec 1996.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,351
Mol. weight: 30.02 kDa
Released: 23 Dec 1996

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

Secondary structure: helices and β-sheets

1CDW contains 5 α-helices and 12 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: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	159	1
β-strand	160-169	10	1
α-helix	176-182	7
β-strand	186-188	3	1
β-strand	195-201	7	1
β-strand	204-210	7	1
β-strand	214-218	5	1
α-helix	223-240	18
β-strand	247-259	13	1
β-strand	264	1	2
α-helix	266-272	7
β-strand	277-278	2	1
β-strand	287-291	5	1
β-strand	296-300	5	1
β-strand	305-309	5	1
α-helix	314-329	16
β-strand	332	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(cptpgpcptpaptpapapapapgpgpcptpg)-3')	B	DNA	16
DNA (5'-d(cpapgpcpcptptptptpaptpapgpcpapg)-3')	C	DNA	16
Protein (tata binding protein (tbp))	A	protein	179	Homo sapiens	P20226 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1CDW_1 DNA (5'-D(*CP*TP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*CP*TP*G)-3') (chains B)
CTGCTATAAAAGGCTG

Sequence of entity 2 (C), FASTA

>1CDW_2 DNA (5'-D(*CP*AP*GP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*AP*G)-3') (chains C)
CAGCCTTTTATAGCAG

Sequence of entity 3 (A), FASTA

>1CDW_3 PROTEIN (TATA BINDING PROTEIN (TBP)) (chains A)
SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGK
MVCTGAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQ
QFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK

Primary citation

Crystal structure of a human TATA box-binding protein/TATA element complex. Nikolov, D.B., Chen, H., Halay, E.D. et al. Proc Natl Acad Sci U S A (1996) 93:4862-4867. DOI 10.1073/pnas.93.10.4862 · PubMed

Other PDB entries of the same protein (UniProt P20226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ROC 1.9 Å, Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter
1NVP 2.1 Å, Human tfiia/tbp/dna complex
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

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