8ENK: UAP56

Crystal structure of UAP56 in complex with Tho1, the yeast homolog of human SARNP. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Aug 2023.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae, synthetic construct
Chains: 5
Atoms: 6,879
Mol. weight: 106.72 kDa
Ligands: BEF, MG, ADP
Released: 16 Aug 2023

Explore 8ENK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ENK contains 41 α-helices and 32 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
α-helix	54-62	9
α-helix	70-80	11
β-strand	85-88	4	1
α-helix	95-106	12
β-strand	116-119	4	1
α-helix	123-136	14
β-strand	145-148	4	1
α-helix	154-163	10
β-strand	168-171	4	1
α-helix	173-181	9
β-strand	192-196	5	1
α-helix	198-203	6
α-helix	205-216	12
β-strand	223-228	6	1
α-helix	236-240	5
β-strand	247-249	3	1
α-helix	254-257	4
β-strand	262-268	7	2
α-helix	271-284	14
β-strand	289-293	5	2
α-helix	297-309	13
β-strand	314-317	4	2
β-strand	319	1	3
β-strand	321	1	3
α-helix	323-334	12
β-strand	340-343	4	2
α-helix	345-347	3
β-strand	356-361	6	2
α-helix	368-375	8
α-helix	380-382	3
β-strand	385-391	7	2
α-helix	394-407	14
β-strand	412-413	2	2
α-helix	414-415	2

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
α-helix	54-62	9
α-helix	70-79	10
β-strand	85-88	4	4
α-helix	95-106	12
β-strand	116-119	4	4
α-helix	123-136	14
β-strand	145-148	4	4
α-helix	154-163	10
β-strand	168-171	4	4
α-helix	173-182	10
β-strand	192-196	5	4
α-helix	198-203	6
α-helix	205-216	12
β-strand	223-228	6	4
α-helix	236-240	5
β-strand	247-249	3	4
α-helix	254-256	3
β-strand	262-268	7	5
α-helix	271-284	14
β-strand	289-293	5	5
α-helix	297-309	13
β-strand	314-317	4	5
β-strand	319	1	6
β-strand	321	1	6
α-helix	323-334	12
β-strand	340-343	4	5
α-helix	345-347	3
β-strand	356-361	6	5
α-helix	368-375	8
α-helix	380-382	3
β-strand	385-391	7	5
α-helix	394-407	14
β-strand	412-413	2	5
α-helix	414-415	2

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	124-142	19
α-helix	147-162	16
α-helix	170-174	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spliceosome RNA helicase DDX39B	A, B	protein	390	Homo sapiens	Q13838 (AlphaFold model)
Protein THO1	E	protein	61	Saccharomyces cerevisiae	P40040 (AlphaFold model)
RNA	M, N	RNA	15	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8ENK_1 Spliceosome RNA helicase DDX39B (chains A, B)
GAMGSSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV
FVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE
EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT
PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKL
FDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR
RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK
ILNDVQDRFEVNISELPDEIDISSYIEQTR

Sequence of entity 2 (E), FASTA

>8ENK_2 Protein THO1 (chains E)
GAMGSEEIKAKALDLLNKKLHRANKFGQDQADIDSLQRQINRVEKFGVDLNSKLAEELGL
V

Sequence of entity 3 (M, N), FASTA

>8ENK_3 RNA (chains M, N)
UUUUUUUUUUUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	2
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Xie, Y., Gao, S., Zhang, K. et al. Cell Rep (2023) 42:112988-112988. DOI 10.1016/j.celrep.2023.112988 · PubMed

Other PDB entries of the same protein (UniProt Q13838 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1T5I 1.9 Å, Crystal structure of the C-terminal domain of UAP56
1T6N 1.94 Å, Crystal structure of the N-terminal domain of human UAP56
1XTI 1.95 Å, Structure of Wildtype human UAP56
1XTK 2.4 Å, structure of DECD to DEAD mutation of human UAP56
9RV1 2.62 Å, Cryo-EM structure of the human UAP56-RNA - SAC3D1-PCID2-SEM1 complex
1XTJ 2.7 Å, structure of human UAP56 in complex with ADP
9DLP 2.79 Å, Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56)
9T6L 2.9 Å, Cryo-EM structure of the human LENG8-PCID2-DSS1 complex bound to UAP56 and RRP1B
9DLV 2.97 Å, Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to DDX39B(UAP56)
9T6N 3.0 Å, Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56
9DLR 3.08 Å, Cryo-EM structure of the human TREX-2.1 complex (LENG8/PCID2/DSS1) bound to the…
7APK 3.3 Å, Structure of the human THO - UAP56 complex

Browse structure collections

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