5KVY: Two tandem rrm domains of PUF60

Crystal structure of the two tandem rrm domains of PUF60 bound to a portion of an adml pre-mRNA 3' splice site analog. Determined by X-ray diffraction at 1.95 Å resolution. Released 23 Aug 2017.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,314
Mol. weight: 55.71 kDa
Released: 23 Aug 2017

Explore 5KVY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KVY contains 14 α-helices and 28 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.

Chains A and B: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	118-128	11
β-strand	130-134	5	1
α-helix	142-149	8
α-helix	150-152	3
β-strand	155-160	6	1
β-strand	163	1	2
β-strand	168	1	2
β-strand	172-177	6	1
α-helix	180-190	11
β-strand	194-195	2	3
β-strand	198-199	2	3
β-strand	201-203	3	1
α-helix	212-222	11
β-strand	227-231	5	4
α-helix	239-246	8
β-strand	252-259	8	4
β-strand	266-274	9	4
α-helix	277-287	11
β-strand	291-292	2	5
β-strand	295-296	2	5
β-strand	298-301	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly(U)-binding-splicing factor PUF60	A, B	protein	216	Homo sapiens	Q9UHX1 (AlphaFold model)
DNA (30-mer)	C	DNA	30	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5KVY_1 Poly(U)-binding-splicing factor PUF60 (chains A, B)
GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM
SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE
EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS
QDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG

Sequence of entity 2 (C), FASTA

>5KVY_2 DNA (30-MER) (chains C)
GAUGUCAUACUUAUCCUGUCCCUUUUUUUU

Primary citation

Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60. Hsiao, H.T., Crichlow, G.V., Murphy, J.W. et al. PLoS One (2020) 15:e0242725-e0242725. DOI 10.1371/journal.pone.0242725 · PubMed

Other PDB entries of the same protein (UniProt Q9UHX1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UE2 1.23 Å, Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa…
3US5 1.38 Å, Crystal structure of a RNA-binding domain of a poly-U binding splicing factor 60KDa…
7Z3X 1.65 Å, Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA
5KW6 1.91 Å, Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Splice Site Analogue with a…
6LUR 2.0 Å, Human PUF60 UHM domain (thioredoxin fusion) in complex with a small molecule binder
7Q8A 2.05 Å, Crystal structure of tandem domain RRM1-2 of FUBP-interacting repressor (FIR) bound to…
2QFJ 2.1 Å, Crystal Structure of First Two RRM Domains of FIR Bound to ssDNA from a Portion of FUSE
5KW1 2.1 Å, Crystal Structure of the Two Tandem RRM Domains of PUF60 Bound to a Modified AdML…
3DXB 2.2 Å, Structure of the UHM domain of Puf60 fused to thioredoxin
3UWT 2.5 Å, Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa…
5KWQ 2.8 Å, Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60
2DNY Solution structure of the third RNA binding domain of FBP-interacting repressor, SIAHBP1

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