4YGX: D. melanogaster Ssu72+Symplekin

Crystal Structure of D. melanogaster Ssu72+Symplekin bound to cis peptidomimetic CTD phospho-Ser5 peptide. Determined by X-ray diffraction at 2.95 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Drosophila melanogaster, synthetic construct
Chains: 5
Atoms: 8,165
Mol. weight: 122.51 kDa
Released: 16 Sept 2015

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

Secondary structure: helices and β-sheets

4YGX contains 63 α-helices and 16 β-strands across 4 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: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	22-37	16
α-helix	42-54	13
α-helix	55-59	5
α-helix	61-64	4
α-helix	68-72	5
α-helix	73-75	3
α-helix	80-96	17
α-helix	98-100	3
α-helix	101-111	11
α-helix	117-138	22
α-helix	146-164	19
α-helix	165-167	3
α-helix	171-187	17
α-helix	204-206	3
α-helix	216-234	19
α-helix	241-257	17
α-helix	259-261	3
α-helix	262-274	13
α-helix	282-300	19
α-helix	303-308	6
α-helix	309-318	10
α-helix	323-329	7
α-helix	331-332	2
α-helix	335-349	15

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	1
α-helix	19-28	10
β-strand	33-38	6	1
β-strand	43-45	3	2
β-strand	54-56	3	2
α-helix	62-73	12
α-helix	76-79	4
α-helix	82-92	11
β-strand	98	1	1
β-strand	108-111	4	1
α-helix	114-126	13
α-helix	128-129	2
β-strand	134-139	6	1
α-helix	146-164	19
α-helix	169-183	15
β-strand	189-194	6	1

Chain C: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	43-53	11
α-helix	54-59	6
α-helix	61-64	4
α-helix	68-72	5
α-helix	73-76	4
α-helix	80-96	17
α-helix	98-100	3
α-helix	101-111	11
α-helix	117-138	22
α-helix	146-164	19
α-helix	165-167	3
α-helix	171-187	17
α-helix	204-206	3
α-helix	216-234	19
α-helix	241-257	17
α-helix	259-261	3
α-helix	262-274	13
α-helix	282-300	19
α-helix	303-308	6
α-helix	309-318	10
α-helix	323-329	7
α-helix	331-332	2
α-helix	335-349	15

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	3
α-helix	19-29	11
β-strand	33-38	6	3
β-strand	43-45	3	4
β-strand	54-56	3	4
α-helix	62-73	12
α-helix	76-79	4
α-helix	82-92	11
β-strand	98	1	3
α-helix	99-101	3
β-strand	108-111	4	3
α-helix	114-126	13
β-strand	134-139	6	3
α-helix	146-164	19
α-helix	169-183	15
β-strand	189-194	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Symplekin	A, C	protein	339	Drosophila melanogaster	Q8MSU4 (AlphaFold model)
LD40846p	B, D	protein	200	Drosophila melanogaster	Q9VWE4 (AlphaFold model)
cis peptidomimetic CTD phospho-Ser5 peptide	E	protein	12	synthetic construct

Sequence of entity 1 (A, C), FASTA

>4YGX_1 Symplekin (chains A, C)
GPGSGMTDEKTATARAKVVDWCNELVIASPSTKCELLAKVQETVLGSCAELAEEFLESVL
SLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYK
NGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFAD
EDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLC
TIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTI
RGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAAQ

Sequence of entity 2 (B, D), FASTA

>4YGX_2 LD40846p (chains B, D)
GPGSGMTDPSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNV
YEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEER
VYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDE
LIQEFEERRKRVILHSVLFY

Sequence of entity 3 (E), FASTA

>4YGX_3 cis peptidomimetic CTD phospho-Ser5 peptide (chains E)
XSPYSPTXSYSX

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 Q8MSU4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IMI 2.35 Å, Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the…
3GS3 2.4 Å, Structure of the N-terminal HEAT Domain of Symplekin from D. melanogaster
6NPW 2.49 Å, SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide
4IMJ 2.58 Å, Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine-tune the…

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