6NPW: SSu72/Sympk

SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide. Determined by X-ray diffraction at 2.49 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 2.49 Å
Organisms: Drosophila melanogaster, Saccharomyces cerevisiae RM11-1a
Chains: 5
Atoms: 8,452
Mol. weight: 123.49 kDa
Ligands: PO4
Released: 24 Apr 2019

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

Secondary structure: helices and β-sheets

6NPW contains 65 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: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	22-37	16
α-helix	42-54	13
α-helix	55-59	5
α-helix	61-63	3
α-helix	65-67	3
α-helix	68-72	5
α-helix	73-76	4
α-helix	80-96	17
α-helix	98-103	6
α-helix	105-111	7
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	323-327	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	43-46	4	2
β-strand	53-56	4	2
α-helix	62-67	6
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	114-125	12
β-strand	134-139	6	1
α-helix	146-164	19
α-helix	169-184	16
β-strand	190-194	5	1

Chain C: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	45-54	10
α-helix	55-59	5
α-helix	68-72	5
α-helix	73-76	4
α-helix	81-96	16
α-helix	98-100	3
α-helix	101-104	4
α-helix	106-111	6
α-helix	117-139	23
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	335-348	14

Chain D: 9 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	82-90	9
β-strand	98	1	3
α-helix	99-101	3
β-strand	108-111	4	3
α-helix	114-125	12
α-helix	128-129	2
β-strand	134-139	6	3
α-helix	146-164	19
α-helix	169-184	16
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)
Ssu72 ortholog, LD40846p	B, D	protein	200	Drosophila melanogaster	Q9VWE4 (AlphaFold model)
Ser2/Ser5 phosphorylated peptide	E	protein	19	Saccharomyces cerevisiae RM11-1a	P04050 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6NPW_1 Symplekin (chains A, C)
GPGSGMTDEKTATARAKVVDWCNELVIASPSTKCELLAKVQETVLGSCAELAEEFLESVL
SLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYK
NGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFAD
EDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLC
TIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTI
RGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAAQ

Sequence of entity 2 (B, D), FASTA

>6NPW_2 Ssu72 ortholog, LD40846p (chains B, D)
GPGSGMTDPSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNV
YEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEER
VYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDE
LIQEFEERRKRVILHSVLFY

Sequence of entity 3 (E), FASTA

>6NPW_3 Ser2/Ser5 phosphorylated peptide (chains E)
SPSYSPTSPSYSPTSPSYS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Primary citation

Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription. Irani, S., Sipe, S.N., Yang, W. et al. J Biol Chem (2019) 294:8592-8605. DOI 10.1074/jbc.RA119.007697 · 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
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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