4YGY: Human Scp1

Crystal Structure of Human Scp1 bound to trans-proline peptidomimetic CTD phospho-Ser5 peptide. Determined by X-ray diffraction at 2.36 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 2.36 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 3,044
Mol. weight: 45.71 kDa
Ligands: MG
Released: 16 Sept 2015

Explore 4YGY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YGY contains 24 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: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	81-84	4
α-helix	85-87	3
β-strand	92-95	4	1
β-strand	98	1	2
β-strand	102-105	4	2
β-strand	114-120	7	2
β-strand	123-131	9	2
α-helix	132	1
α-helix	135-145	11
β-strand	147-151	5	1
α-helix	156-166	11
β-strand	172-176	5	1
α-helix	178-180	3
β-strand	182-184	3	3
β-strand	187-189	3	3
α-helix	192-194	3
α-helix	199-201	3
β-strand	202-206	5	1
α-helix	209-212	4
α-helix	216-218	3
β-strand	219-221	3	1
α-helix	233-244	12
α-helix	251-254	4

Chain B: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	81-84	4
α-helix	91	1
β-strand	92-95	4	4
β-strand	98	1	5
β-strand	102-105	4	5
β-strand	114-120	7	5
β-strand	123-131	9	5
α-helix	132	1
α-helix	135-145	11
β-strand	147-151	5	4
α-helix	156-166	11
β-strand	172-176	5	4
α-helix	178-180	3
β-strand	182-184	3	6
β-strand	187-189	3	6
α-helix	192-194	3
α-helix	199-201	3
β-strand	202-206	5	4
α-helix	209-212	4
α-helix	216-218	3
β-strand	219-221	3	4
α-helix	233-244	12
α-helix	251-254	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1	A, B	protein	189	Homo sapiens	Q9GZU7 (AlphaFold model)
peptidomimetic CTD phospho-Ser5 peptide	C, D	protein	12	synthetic construct

Sequence of entity 1 (A, B), FASTA

>4YGY_1 Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (chains A, B)
GSHGQYLLPEAKAQDSDKICVVINLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKR
PHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDL
SRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYS
VLRQPRPGS

Sequence of entity 2 (C, D), FASTA

>4YGY_2 peptidomimetic CTD phospho-Ser5 peptide (chains C, D)
XSPYSPTXSYSX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. Mayfield, J.E., Fan, S., Wei, S. et al. ACS Chem Biol (2015) 10:2405-2414. DOI 10.1021/acschembio.5b00296 · PubMed

Other PDB entries of the same protein (UniProt Q9GZU7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2GHT 1.8 Å, CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA…
2GHQ 2.05 Å, CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA…
1TA0 2.1 Å, Three-dimensional structure of a RNA-polymerase II binding protein with associated ligand.
4YH1 2.2 Å, Structure of Human Scp1 bound to cis-proline peptidomimetic CTD phospho-Ser5 peptide
1T9Z 2.3 Å, Three-dimensional structure of a RNA-polymerase II binding protein.
3L0Y 2.3 Å, Crystal structure OF SCP1 phosphatase D98A mutant
3L0B 2.35 Å, Crystal structure of SCP1 phosphatase D206A mutant phosphoryl-intermediate
3PGL 2.35 Å, Crystal structure of human small C-terminal domain phosphatase 1 (Scp1) bound to…
3L0C 2.45 Å, Crystal structure of SCP1 phosphatase D206A mutant with trapped inorganic phosphate
6DU3 2.58 Å, Structure of Scp1 D96N bound to REST-pS861/4 peptide

Browse structure collections

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