4IMI: Symplekin

Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the Phosphatase Activity of Ssu72. Determined by X-ray diffraction at 2.35 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Drosophila melanogaster, Synthetic
Chains: 5
Atoms: 8,381
Mol. weight: 123.49 kDa
Ligands: PO4
Released: 7 Aug 2013

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

Secondary structure: helices and β-sheets

4IMI contains 64 α-helices and 16 β-strands across 5 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	61-67	7
α-helix	68-72	5
α-helix	73-75	3
α-helix	80-96	17
α-helix	98-103	6
α-helix	105-111	7
α-helix	117-140	24
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	323-327	5
α-helix	331-332	2
α-helix	335-348	14

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	1
α-helix	19-29	11
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
α-helix	99-101	3
β-strand	108-111	4	1
α-helix	114-126	13
β-strand	134-139	6	1
α-helix	146-165	20
α-helix	169-184	16
β-strand	190-194	5	1

Chain C: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	43-53	11
α-helix	54-59	6
α-helix	61-65	5
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	117-140	24
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	323-327	5
α-helix	331-332	2
α-helix	335-348	14

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	43-49	7	4
β-strand	52-56	5	4
α-helix	62-73	12
α-helix	76-79	4
α-helix	82-90	9
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	169-184	16
β-strand	190-194	5	3

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Symplekin	A, C	protein	339	Drosophila melanogaster	Q8MSU4 (AlphaFold model)
CG14216	B, D	protein	200	Drosophila melanogaster	Q9VWE4 (AlphaFold model)
CTD	F	protein	19	Synthetic

Sequence of entity 1 (A, C), FASTA

>4IMI_1 Symplekin (chains A, C)
GPGSGMTDEKTATARAKVVDWCNELVIASPSTKCELLAKVQETVLGSCAELAEEFLESVL
SLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYK
NGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFAD
EDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLC
TIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTI
RGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAAQ

Sequence of entity 2 (B, D), FASTA

>4IMI_2 CG14216 (chains B, D)
GPGSGMTDPSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNV
YEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEER
VYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDE
LIQEFEERRKRVILHSVLFY

Sequence of entity 3 (F), FASTA

>4IMI_3 CTD (chains F)
SPSYSPTSPSYSPTSPSYS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Primary citation

Novel Modifications on C-terminal Domain of RNA Polymerase II Can Fine-tune the Phosphatase Activity of Ssu72. Luo, Y., Yogesha, S.D., Cannon, J.R. et al. ACS Chem Biol (2013) 8:2042-2052. DOI 10.1021/cb400229c · PubMed

Other PDB entries of the same protein (UniProt Q8MSU4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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…
4YGX 2.95 Å, Crystal Structure of D. melanogaster Ssu72+Symplekin bound to cis peptidomimetic CTD…

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