6Q5Y: SPOC domain of human PHF3

Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser5. Determined by X-ray diffraction at 2.85 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,918
Mol. weight: 76.4 kDa
Released: 15 Jul 2020

Explore 6Q5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q5Y contains 16 α-helices and 32 β-strands across 6 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1209-1215	7	1
β-strand	1219-1227	9	1
α-helix	1236-1238	3
β-strand	1242-1249	8	1
α-helix	1256-1261	6
β-strand	1271-1276	6	1
α-helix	1279-1295	17
β-strand	1298-1301	4	1
β-strand	1312-1316	5	1
α-helix	1324-1326	3
β-strand	1341-1345	5	1

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	1209-1214	6	2
β-strand	1220-1229	10	2
β-strand	1242-1249	8	2
α-helix	1251-1261	11
β-strand	1270-1276	7	2
α-helix	1279-1295	17
β-strand	1298-1301	4	2
β-strand	1308	1	3
β-strand	1312-1316	5	2
α-helix	1320-1323	4
α-helix	1324-1326	3
β-strand	1341-1346	6	2
β-strand	1348	1	3

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1209-1214	6	4
β-strand	1220-1230	11	4
β-strand	1242-1249	8	4
α-helix	1251-1261	11
β-strand	1268-1276	9	4
α-helix	1279-1295	17
β-strand	1298-1301	4	4
β-strand	1308-1316	9	4
α-helix	1321-1323	3
α-helix	1324-1326	3
α-helix	1333-1335	3
β-strand	1341-1348	8	4

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1209-1214	6	5
β-strand	1220-1230	11	5
β-strand	1242-1249	8	5
α-helix	1251-1261	11
β-strand	1267-1276	10	5
α-helix	1279-1295	17
β-strand	1298-1301	4	5
β-strand	1308-1316	9	5
α-helix	1321-1323	3
β-strand	1341-1349	9	5

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12	1	4

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11-12	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 3	A, B, C, D	protein	162	Homo sapiens	Q92576 (AlphaFold model)
pSer2pSer5	E, F	protein	14	Homo sapiens	P24928 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6Q5Y_1 PHD finger protein 3 (chains A, B, C, D)
GAMGSTFLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTV
WDYVEKIKASGTKEICVVRFTPVTEEDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLI
PLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIRQKLKRQHS

Sequence of entity 2 (E, F), FASTA

>6Q5Y_2 pSer2pSer5 (chains E, F)
YSPTSPSYSPTSPS

Primary citation

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Appel, L.M., Franke, V., Bruno, M. et al. Nat Commun (2021) 12:6078. DOI 10.1038/s41467-021-26360-2

Other PDB entries of the same protein (UniProt Q92576 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6IC9 1.75 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
6IC8 1.93 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
6Q2V 2.59 Å, Crystal structure of SPOC domain of human PHD-finger protein 3 (PHF3)
2DME Solution structure of the TFIIS domain II of human PHD finger protein 3

Browse structure collections

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