5WXH: TAF3 PHD finger

Crystal structure of TAF3 PHD finger bound to H3K4me3. Determined by X-ray diffraction at 1.3 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,286
Mol. weight: 16.48 kDa
Ligands: ZN
Released: 16 Aug 2017

Explore 5WXH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WXH contains 5 α-helices and 14 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	858-860	3	1
β-strand	866-868	3	1
β-strand	869	1	2
β-strand	876	1	2
β-strand	882-884	3	3
β-strand	891-893	3	3
α-helix	894-897	4
α-helix	902-904	3
α-helix	912-915	4

Chain C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	858-860	3	4
β-strand	866-868	3	4
β-strand	869-870	2	5
β-strand	875-876	2	5
β-strand	882-884	3	6
β-strand	891-893	3	6
α-helix	894-897	4
α-helix	902-904	3

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	6

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription initiation factor TFIID subunit 3	A, C	protein	63	Homo sapiens	Q5VWG9 (AlphaFold model)
Histone H3K4me3	D, P	protein	7	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5WXH_1 Transcription initiation factor TFIID subunit 3 (chains A, C)
SMYVIRDEWGNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC
ANK

Sequence of entity 2 (D, P), FASTA

>5WXH_2 Histone H3K4me3 (chains D, P)
ARTKQTA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology. Zhao, S., Yang, M., Zhou, W. et al. Proc Natl Acad Sci U S A (2017) 114:E7245-E7254. DOI 10.1073/pnas.1704155114 · PubMed

Other PDB entries of the same protein (UniProt Q5VWG9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XMY 1.7 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser
5WXG 1.7 Å, Structure of TAF PHD finger domain binds to H3(1-15)K4ac
5C13 2.1 Å, Crystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide
7EGF 3.16 Å, TFIID lobe A subcomplex
7EGB 3.3 Å, TFIID-based holo PIC on SCP promoter
7EG9 3.7 Å, TFIID-based intermediate PIC on SCP promoter
7EGC 3.9 Å, p53-bound TFIID-based holo PIC on HDM2 promoter
7ENA 4.07 Å, TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
7EGA 4.1 Å, TFIID-based intermediate PIC on PUMA promoter
7ENC 4.13 Å, TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
8GXS 4.16 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
7EDX 4.5 Å, p53-bound TFIID-based core PIC on HDM2 promoter

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