3VAJ: U2AF65 variant with BrU5C6 DNA

Structure of U2AF65 variant with BrU5C6 DNA. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,297
Mol. weight: 44.34 kDa
Ligands: CPQ, DIO
Released: 13 Feb 2013

Explore 3VAJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VAJ contains 15 α-helices and 24 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.

Chain A: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	150-154	5	1
α-helix	156-157	2
α-helix	162-175	14
β-strand	186-192	7	1
β-strand	197-202	6	1
α-helix	205-211	7
α-helix	212-214	3
β-strand	218-219	2	2
β-strand	222-223	2	2
β-strand	225-227	3	1
α-helix	234-235	2
β-strand	261-264	4	3
α-helix	272-280	9
β-strand	285-292	8	3
β-strand	299-307	9	3
α-helix	312-320	9
β-strand	324-325	2	4
β-strand	328-329	2	4
β-strand	331-334	4	3

Chain B: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	147-149	3
β-strand	150-154	5	5
α-helix	156-157	2
α-helix	162-175	14
β-strand	186-192	7	5
β-strand	197-202	6	5
α-helix	205-211	7
α-helix	212-214	3
β-strand	218-219	2	6
β-strand	222-223	2	6
β-strand	225-227	3	5
β-strand	261-264	4	7
α-helix	272-279	8
β-strand	285-293	9	7
β-strand	298-307	10	7
α-helix	310-312	3
α-helix	313-320	8
β-strand	324-325	2	8
β-strand	328-329	2	8
β-strand	331-334	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Splicing factor U2AF 65 kDa subunit	A, B	protein	174	Homo sapiens	P26368 (AlphaFold model)
DNA (5'-d(upupupup(bru)pcp*u)-3')	E, P	DNA	7

Sequence of entity 1 (A, B), FASTA

>3VAJ_1 Splicing factor U2AF 65 kDa subunit (chains A, B)
GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF
RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSF
GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS

Sequence of entity 2 (E, P), FASTA

>3VAJ_2 DNA (5'-D(*UP*UP*UP*UP*(BRU)P*CP*U)-3') (chains E, P)
UUUUUCU

Ligands and cofactors

ID	Name	Formula	Copies
CPQ	N,n-BIS(3-D-gluconamidopropyl)deoxycholamide	C42 H75 N3 O15	1
DIO	1,4-diethylene dioxide	C4 H8 O2	5

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Jenkins, J.L., Agrawal, A.A., Gupta, A. et al. Nucleic Acids Res (2013) 41:3859-3873. DOI 10.1093/nar/gkt046 · PubMed

Other PDB entries of the same protein (UniProt P26368 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W0G 1.07 Å, Structure of U2AF65 (U2AF2) RRM1 at 1.07 resolution
5W0H 1.11 Å, Structure of U2AF65 (U2AF2) RRM2 at 1.11 Angstrom Resolution
6XLV 1.4 Å, Crystal structure of leukemia-associated N196K mutant of U2AF65 bound to AdML splice site
9C7A 1.4 Å, Crystal structure of R149W neurodevelopmental disease-associated U2AF2 variant
9C7B 1.4 Å, Crystal structure of R150H neurodevelopmental disease-associated U2AF2 variant
2HZC 1.47 Å, Crystal structure of the N-terminal RRM of the U2AF large subunit
7S3A 1.48 Å, Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide
5EV3 1.5 Å, Structure III of Intact U2AF65 Recognizing the 3' Splice Site Signal
6XLW 1.5 Å, Crystal structure of U2AF65 bound to AdML splice site sequence
7S3C 1.51 Å, Crystal structure of intact U2AF65 RRM-region bound to AdML-A5 oligonucleotide
5EV4 1.57 Å, Structure IV of Intact U2AF65 Recognizing the 3' Splice Site Signal
6XLX 1.7 Å, Crystal structure of cancer-associated G301D mutant of U2AF65 bound to AdML splice site

Browse structure collections

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