5XFP: Binary complex of PHF1 and a double stranded DNA

Binary complex of PHF1 and a double stranded DNA. Determined by X-ray diffraction at 2.3 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,034
Mol. weight: 122.07 kDa
Ligands: ZN
Released: 13 Sept 2017

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

Secondary structure: helices and β-sheets

5XFP contains 56 α-helices and 57 β-strands across 3 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: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	1
β-strand	46-55	10	1
β-strand	60-65	6	1
β-strand	70-74	5	1
α-helix	75-77	3
β-strand	78-80	3	1
α-helix	81-83	3
β-strand	90	1	2
β-strand	99	1	3
β-strand	102	1	3
β-strand	104-106	3	2
β-strand	113-115	3	2
α-helix	116-118	3
α-helix	122-125	4
α-helix	137-144	8
α-helix	155-163	9
α-helix	171-173	3
β-strand	176	1	4
β-strand	183	1	4
β-strand	201-203	3	5
β-strand	204	1	6
β-strand	210-212	3	5
α-helix	213-215	3
α-helix	222-224	3
β-strand	230-233	4	6
α-helix	235-238	4
β-strand	243-246	4	6
α-helix	247-250	4
α-helix	251-266	16
β-strand	271-272	2	7
α-helix	273-277	5
α-helix	278-283	6
α-helix	285-288	4
α-helix	291-295	5
α-helix	301-311	11
β-strand	316-318	3	7
α-helix	319-322	4
β-strand	328-331	4	7
α-helix	336-338	3

Chain B: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	8
β-strand	46-55	10	8
β-strand	60-65	6	8
β-strand	70-74	5	8
α-helix	75-77	3
β-strand	78-80	3	8
α-helix	81-83	3
β-strand	90	1	9
β-strand	104-106	3	9
β-strand	113-115	3	9
α-helix	116-118	3
α-helix	122-125	4
α-helix	137-144	8
α-helix	155-163	9
α-helix	171-173	3
β-strand	176	1	10
β-strand	183	1	10
β-strand	201-203	3	11
β-strand	204	1	12
β-strand	210-212	3	11
α-helix	213-215	3
α-helix	222-224	3
β-strand	230-233	4	12
α-helix	235-238	4
β-strand	243-246	4	12
α-helix	247-250	4
α-helix	251-266	16
β-strand	271-272	2	13
α-helix	273-277	5
α-helix	278-283	6
α-helix	286-288	3
α-helix	291-295	5
α-helix	298-311	14
β-strand	316-318	3	13
α-helix	319-322	4
β-strand	328-331	4	13

Chain E: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	14
β-strand	46-55	10	14
β-strand	60-65	6	14
β-strand	70-74	5	14
α-helix	75-77	3
β-strand	78-80	3	14
β-strand	99	1	15
β-strand	102	1	15
β-strand	104-106	3	16
β-strand	113-115	3	16
α-helix	116-118	3
α-helix	122-125	4
α-helix	137-144	8
α-helix	155-163	9
α-helix	171-173	3
β-strand	176	1	17
β-strand	183	1	17
β-strand	201-203	3	18
β-strand	204	1	19
β-strand	210-212	3	18
α-helix	213-215	3
α-helix	222-224	3
β-strand	230-233	4	19
α-helix	235-238	4
β-strand	243-246	4	19
α-helix	247-250	4
α-helix	251-266	16
β-strand	271-272	2	20
α-helix	273-277	5
α-helix	278-283	6
α-helix	285-287	3
α-helix	291-295	5
α-helix	297	1
α-helix	300-311	12
β-strand	316-319	4	20
β-strand	328-331	4	20
α-helix	332-334	3
α-helix	335-337	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 1	A, B, E	protein	336	Homo sapiens	O43189 (AlphaFold model)
DNA (5'-d(gpgpgpcpgpgpcpcpgpcpcpcp*t)-3')	C, D	DNA	13	synthetic construct

Sequence of entity 1 (A, B, E), FASTA

>5XFP_1 PHD finger protein 1 (chains A, B, E)
SGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALP
GEELLCCVCRSETVVPGNRLVSCEKCRHAYHQDCHVPRAPAPGEGEGTSWVCRQCVFAIA
TKRGGALKKGPYARAMLGMKLSLPYGLKGLDWDAGHLSNRQQSYCYCGGPGEWNLKMLQC
RSCLQWFHEACTQCLSKPLLYGDRFYEFECCVCRGGPEKVRRLQLRWVDVAHLVLYHLSV
CCKKKYFDFDREILPFTSENWDSLLLGELSDTPKGERSSRLLSALNSHKDRFISGREIKK
RKCLFGLHARMPPPVEPPTGDGALTSFPSGQGPGGG

Sequence of entity 2 (C, D), FASTA

>5XFP_2 DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') (chains C, D)
GGGCGGCCGCCCT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

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

Primary citation

Polycomb-like proteins link the PRC2 complex to CpG islands. Li, H., Liefke, R., Jiang, J. et al. Nature (2017) 549:287-291. DOI 10.1038/nature23881 · PubMed

Other PDB entries of the same protein (UniProt O43189 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WAV 1.7 Å, Crystal structure of PHF1 in complex with H3K36me3 substitution
6WAT 1.8 Å, complex structure of PHF1
4HCZ 1.85 Å, PHF1 Tudor in complex with H3K36me3
7LKY 1.85 Å, Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
5XFN 1.9 Å, Structure of the N-terminal domains of PHF1
5XFO 1.9 Å, Structure of the N-terminal domains of PHF1
8H43 2.3 Å, Crystal structure of PHF1 Tudor domain in complex with hit 1
2E5P Solution structure of the TUDOR domain of PHD finger protein 1 (PHF1 protein)
2M0O The solution structure of human PHF1 in complex with H3K36me3

Browse structure collections

About this viewer

MolViewer shows 5XFP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.