5XMY: TAF3 PHD finger

Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser. Determined by X-ray diffraction at 1.7 Å resolution. Released 28 Nov 2018.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,215
Mol. weight: 16.48 kDa
Ligands: ZN
Released: 28 Nov 2018

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

Secondary structure: helices and β-sheets

5XMY 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	895-897	3
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 peptide H3(1-15)K4me3Q5ser	D, P	protein	7	synthetic construct

Sequence of entity 1 (A, C), FASTA

>5XMY_1 Transcription initiation factor TFIID subunit 3 (chains A, C)
SMYVIRDEWGNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKC
ANK

Sequence of entity 2 (D, P), FASTA

>5XMY_2 Histone peptide H3(1-15)K4me3Q5ser (chains D, P)
ARTKQTA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser. Zhao, S., Zhang, B., Li, H. To be published.

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

5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
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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