6SLO: PUF60 UHM domain

Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine. Determined by X-ray diffraction at 1.94 Å resolution. Released 9 Sept 2020.

Method: X-ray diffraction
Resolution: 1.94 Å
Organisms: Citrobacter freundii MGH 56, Homo sapiens
Chains: 4
Atoms: 7,231
Mol. weight: 99.66 kDa
Ligands: LJT, MG
Released: 9 Sept 2020

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

Secondary structure: helices and β-sheets

6SLO contains 37 α-helices and 48 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: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	349-351	3	1
α-helix	356	1
α-helix	357-361	5
β-strand	367-372	6	1
α-helix	377-392	16
β-strand	398-403	6	1
α-helix	411-414	4
β-strand	419	1	2
β-strand	421-426	6	1
β-strand	429-435	7	1
α-helix	440-451	12
β-strand	460-464	5	3
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	3
β-strand	508-516	9	3
α-helix	519-529	11
β-strand	533-534	2	4
β-strand	537-538	2	4
β-strand	540-543	4	3
α-helix	546-550	5

Chain B: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	5
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	5
α-helix	377-392	16
β-strand	397-403	7	5
α-helix	411-414	4
β-strand	419	1	6
β-strand	421-426	6	5
β-strand	429-435	7	5
α-helix	440-451	12
β-strand	460-464	5	7
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	7
β-strand	508-516	9	7
α-helix	519-529	11
β-strand	533-534	2	8
β-strand	537-538	2	8
β-strand	540-543	4	7
α-helix	546-550	5

Chain C: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	9
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	9
α-helix	377-392	16
β-strand	397-403	7	9
α-helix	411-414	4
β-strand	421-426	6	9
β-strand	429-435	7	9
α-helix	440-450	11
β-strand	457	1	2
β-strand	460-464	5	10
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	10
β-strand	508-516	9	10
α-helix	519-529	11
β-strand	533-534	2	11
β-strand	537-538	2	11
β-strand	540-543	4	10
α-helix	546-550	5

Chain D: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	12
α-helix	351	1
α-helix	356	1
α-helix	357-361	5
β-strand	367-372	6	12
α-helix	377-392	16
β-strand	398-403	6	12
α-helix	411-414	4
β-strand	421-426	6	12
β-strand	429-435	7	12
α-helix	440-451	12
β-strand	457	1	6
β-strand	460-464	5	13
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	13
β-strand	508-516	9	13
α-helix	519-529	11
β-strand	533-534	2	14
β-strand	537-538	2	14
β-strand	540-543	4	13
α-helix	546-550	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin,Poly(U)-binding-splicing factor PUF60	A, B, C, D	protein	222	Citrobacter freundii MGH 56, Homo sapiens	P0AA25 (AlphaFold model)

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

>6SLO_1 Thioredoxin,Poly(U)-binding-splicing factor PUF60 (chains A, B, C, D)
MKHHHHHHPMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQ
GKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGS
AMESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFV
EFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLSA

Ligands and cofactors

ID	Name	Formula	Copies
LJT	2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl)propyl]piperazin-1-yl]eth…	C23 H30 Cl N3 O3 S	2
MG	Magnesium ion	Mg	2

Primary citation

Identification of phenothiazine derivatives as UHM-binding inhibitors of early spliceosome assembly. Jagtap, P.K.A., Kubelka, T., Soni, K. et al. Nat Commun (2020) 11:5621-5621. DOI 10.1038/s41467-020-19514-1 · PubMed

Other PDB entries of the same protein (UniProt P0AA25 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HUA 1.1 Å, E. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue
5HR3 1.1 Å, Crystal structure of thioredoxin N106A mutant
5HR2 1.2 Å, Crystal structure of thioredoxin L94A mutant
5HR0 1.31 Å, Crystal structure of thioredoxin E101G mutant
4HU7 1.4 Å, E. coli thioredoxin variant with Pro76 as single proline residue
4HU9 1.55 Å, E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue
4X43 1.65 Å, Structure of proline-free E. coli Thioredoxin
2TRX 1.68 Å, Crystal structure of thioredoxin from escherichia coli at 1.68 Å resolution
6Y4Y 1.75 Å, The crystal structure of human MACROD2 in space group P41212
1KEB 1.8 Å, Crystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin
2EIQ 1.9 Å, Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal…
6Y4Z 1.9 Å, The crystal structure of human MACROD2 in space group P43212

Browse structure collections

About this viewer

MolViewer shows 6SLO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.