7C07 | pdb_00007c07

Crystal structure of yeast U2AF1 complex bound to 5'-AAGGU RNA.

PDB DOI: https://doi.org/10.2210/pdb7C07/pdb
NAKB: 7C07

Classification: SPLICING/RNA
Organism(s): Schizosaccharomyces pombe 972h-, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-30 Released: 2020-09-30
Deposition Author(s): Yoshida, H., Park, S.Y., Urano, T., Obayashi, E.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.285 (Depositor), 0.289 (DCC)
R-Value Work:
0.255 (Depositor), 0.259 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.

Yoshida, H., Park, S.Y., Sakashita, G., Nariai, Y., Kuwasako, K., Muto, Y., Urano, T., Obayashi, E.

(2020) Nat Commun 11: 4744-4744

PubMed: 32958768 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-18559-6
Primary Citation Related Structures:
7C06, 7C07, 7C08

PubMed Abstract:
The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors.

Organizational Affiliation

Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

Macromolecule Content

Total Structure Weight: 314.48 kDa
Atom Count: 18,390
Modeled Residue Count: 2,183
Deposited Residue Count: 2,619
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 23 kDa subunit	A, D, G, J, M A, D, G, J, M, P, S, V, Y	216	Schizosaccharomyces pombe 972h-	Mutation(s): 0 Gene Names: SPAP8A3.06
UniProt
Find proteins for Q09176 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q09176 Go to UniProtKB: Q09176
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09176
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 59 kDa subunit	B, E, H, K, N B, E, H, K, N, Q, T, W, Z	69	Schizosaccharomyces pombe 972h-	Mutation(s): 0 Gene Names: prp2, mis11, SPBC146.07
UniProt
Find proteins for P36629 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P36629 Go to UniProtKB: P36629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36629
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
RNA (5'-R(UAPAPGPGPU)-3')	AA [auth 1] C F I L AA [auth 1], C, F, I, L, O, R, U, X	6	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain SA [auth Y] SDF format, chain RA [auth Y] SDF format, chain QA [auth V] SDF format, chain PA [auth V] SDF format, chain OA [auth S] SDF format, chain NA [auth S] SDF format, chain MA [auth P] SDF format, chain LA [auth P] SDF format, chain KA [auth M] SDF format, chain JA [auth M] SDF format, chain IA [auth J] SDF format, chain HA [auth J] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth A] SDF format, chain BA [auth A] MOL2 format, chain SA [auth Y] MOL2 format, chain RA [auth Y] MOL2 format, chain QA [auth V] MOL2 format, chain PA [auth V] MOL2 format, chain OA [auth S] MOL2 format, chain NA [auth S] MOL2 format, chain MA [auth P] MOL2 format, chain LA [auth P] MOL2 format, chain KA [auth M] MOL2 format, chain JA [auth M] MOL2 format, chain IA [auth J] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain SA [auth Y] mmCIF format, chain RA [auth Y] mmCIF format, chain QA [auth V] mmCIF format, chain PA [auth V] mmCIF format, chain OA [auth S] mmCIF format, chain NA [auth S] mmCIF format, chain MA [auth P] mmCIF format, chain LA [auth P] mmCIF format, chain KA [auth M] mmCIF format, chain JA [auth M] mmCIF format, chain IA [auth J] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A]	BA [auth A] CA [auth A] DA [auth D] EA [auth D] FA [auth G] BA [auth A], CA [auth A], DA [auth D], EA [auth D], FA [auth G], GA [auth G], HA [auth J], IA [auth J], JA [auth M], KA [auth M], LA [auth P], MA [auth P], NA [auth S], OA [auth S], PA [auth V], QA [auth V], RA [auth Y], SA [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain LA [auth P] Focus chain MA [auth P] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth V] Focus chain QA [auth V] Focus chain RA [auth Y] Focus chain SA [auth Y] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain LA [auth P] Focus chain MA [auth P] Focus chain NA [auth S] Focus chain OA [auth S] Focus chain PA [auth V] Focus chain QA [auth V] Focus chain RA [auth Y] Focus chain SA [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.285 (Depositor), 0.289 (DCC)
R-Value Work: 0.255 (Depositor), 0.259 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.487	α = 90
b = 256.947	β = 100.751
c = 94.591	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06086

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2020-10-07
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description