5VDC: Human DPF2 tandem PHD finger domain

Crystal structure of the human DPF2 tandem PHD finger domain. Determined by X-ray diffraction at 1.6 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,121
Mol. weight: 14.7 kDa
Ligands: ZN
Released: 24 May 2017

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

Secondary structure: helices and β-sheets

5VDC contains 6 α-helices and 7 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	13	1	1
β-strand	24-25	2	2
β-strand	32-33	2	2
α-helix	42-47	6
β-strand	61	1	3
α-helix	70-72	3
β-strand	73-75	3	3
β-strand	82-84	3	3
α-helix	91-92	2
α-helix	95-96	2
α-helix	103-109	7
α-helix	110-112	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Zinc finger protein ubi-d4	A	protein	126	Homo sapiens	Q92785 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VDC_1 Zinc finger protein ubi-d4 (chains A)
GMGSNNYCDFCLGDSKINKKTGQPEELVSCSDCGRSGHPSCLQFTPVMMAAVKTYRWQCI
ECKCCNICGTSENDDQLLFCDDCDRGYHMYCLTPSMSEPPEGSWSCHLCLDLLKEKASIY
QNQNSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (GOL, EDO) are not listed.

Primary citation

Histone-binding of DPF2 mediates its repressive role in myeloid differentiation. Huber, F.M., Greenblatt, S.M., Davenport, A.M. et al. Proc Natl Acad Sci U S A (2017) 114:6016-6021. DOI 10.1073/pnas.1700328114 · PubMed

Other PDB entries of the same protein (UniProt Q92785 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3IUF 1.8 Å, Crystal structure of the C2H2-type zinc finger domain of human ubi-d4
5B79 2.6 Å, Crystal structure of DPF2 double PHD finger
6LTH 3.0 Å, Structure of human BAF Base module
9RL4 3.5 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
6LTJ 3.7 Å, Structure of nucleosome-bound human BAF complex
9RN2 4.1 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
9RMC 4.2 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1
9RN1 5.9 Å, Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47…
9A0K A structural model of the endogenoushuman SWI/SNF (BAF) complex bound to the nucleosome…

Browse structure collections

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