4OZ1: Human CAPERalpha UHM

Crystal structure of human CAPERalpha UHM bound to SF3b155 ULM5. Determined by X-ray diffraction at 1.74 Å resolution. Released 14 May 2014.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,108
Mol. weight: 26.85 kDa
Ligands: LYS
Released: 14 May 2014

Explore 4OZ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OZ1 contains 11 α-helices and 13 β-strands across 3 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	413-416	4
β-strand	419-423	5	1
α-helix	436-448	13
β-strand	456-459	4	1
β-strand	468-471	4	1
α-helix	475-485	11
β-strand	489-490	2	2
β-strand	493-494	2	2
β-strand	496-500	5	1
α-helix	502-508	7
α-helix	510-513	4

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	419-423	5	3
α-helix	428-432	5
α-helix	436-448	13
β-strand	456-459	4	3
β-strand	468-471	4	3
α-helix	475-485	11
β-strand	489-490	2	4
β-strand	493-494	2	4
β-strand	496-500	5	3
α-helix	502-508	7
α-helix	510-513	4
α-helix	518-519	2

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	338	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-binding protein 39	A, B	protein	115	Homo sapiens	Q14498 (AlphaFold model)
Splicing factor 3B subunit 1	C	protein	10	Homo sapiens	O75533 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4OZ1_1 RNA-binding protein 39 (chains A, B)
GSVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVY
VKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR

Sequence of entity 2 (C), FASTA

>4OZ1_2 Splicing factor 3B subunit 1 (chains C)
KRKSRWDETP

Ligands and cofactors

ID	Name	Formula	Copies
LYS	Lysine	C6 H15 N2 O2	1

Water and common crystallization additives (K, CL) are not listed.

Primary citation

Cancer-relevant splicing factor CAPER alpha engages the essential splicing factor SF3b155 in a specific ternary complex. Loerch, S., Maucuer, A., Manceau, V. et al. J Biol Chem (2014) 289:17325-17337. DOI 10.1074/jbc.M114.558825 · PubMed

Other PDB entries of the same protein (UniProt Q14498 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YUD 1.28 Å, Crystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 A…
4OZ0 2.2 Å, Crystal structure of human CAPERalpha U2AF homology motif (apo-state)
6UD7 2.3 Å, Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with…
6UE5 2.61 Å, Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with…
4OO6 2.7 Å, Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma…
6PAI 2.9 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and…
6Q0R 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39
6Q0V 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39
6Q0W 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39
6SJ7 3.54 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam
2JRS Solution NMR Structure of CAPER RRM2 Domain. Northeast Structural Genomics Target HR4730A
2MHN NMR structure of the first RRM domain of the protein RBM39 from Homo sapiens

Browse structure collections

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