5SYB: Human PHF5A

Crystal structure of human PHF5A. Determined by X-ray diffraction at 1.82 Å resolution. Released 7 Sept 2016.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,483
Mol. weight: 25.97 kDa
Ligands: ZN
Released: 7 Sept 2016

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

Secondary structure: helices and β-sheets

5SYB contains 16 α-helices and 22 β-strands across 2 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: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
α-helix	13-15	3
β-strand	18-19	2	2
α-helix	20	1
β-strand	21-22	2	3
α-helix	38	1
β-strand	39-42	4	4
β-strand	44-45	2	2
α-helix	47-50	4
β-strand	57	1	5
β-strand	58	1	3
α-helix	63	1
β-strand	64	1	5
α-helix	65	1
β-strand	67-68	2	3
β-strand	70-72	3	4
α-helix	73-77	5
α-helix	80-83	4
β-strand	88-90	3	1

Chain B: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	6
α-helix	13-15	3
β-strand	18-19	2	7
α-helix	20	1
β-strand	21-22	2	8
α-helix	37-38	2
β-strand	39-42	4	9
β-strand	44-45	2	7
α-helix	52-54	3
β-strand	57	1	10
β-strand	58	1	8
α-helix	63	1
β-strand	64	1	10
α-helix	65	1
β-strand	67-68	2	8
β-strand	70-72	3	9
α-helix	73-77	5
α-helix	80-83	4
β-strand	88-90	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger-like domain-containing protein 5A	A, B	protein	113	Homo sapiens	Q7RTV0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5SYB_1 PHD finger-like domain-containing protein 5A (chains A, B)
GGHMAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPSTLVRICDECNYGSYQGR
CVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

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

Primary citation

Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex. Teng, T., Tsai, J.H., Puyang, X. et al. Nat Commun (2017) 8:15522-15522. DOI 10.1038/ncomms15522 · PubMed

Other PDB entries of the same protein (UniProt Q7RTV0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q4O 2.1 Å, Substrate-bound A-like U2 snRNP
7Q4P 2.15 Å, U2 snRNP after ATP-dependent remodelling
7Q3L 2.21 Å, Human 17S U2 snRNP 5' domain
7B9C 2.4 Å, Structure of a minimal SF3B core in complex with spliceostatin A (form I)
7EVO 2.5 Å, The cryo-EM structure of the human 17S U2 snRNP
7EVN 2.6 Å, The cryo-EM structure of the DDX42-SF3b complex
8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
8HK1 2.7 Å, The cryo-EM structure of human pre-17S U2 snRNP
7DVQ 2.89 Å, Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
7B0I 3.0 Å, Structure of a minimal SF3B core in complex with spliceostatin A (form II)
7B91 3.0 Å, Structure of a minimal SF3B core in complex with pladienolide D (form I)

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