7ZAM | pdb_00007zam

Sam68

PDB DOI: https://doi.org/10.2210/pdb7ZAM/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-03-22 Released: 2023-02-01
Deposition Author(s): Nadal, M., Fuentes-Prior, P.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.214 (Depositor), 0.197 (DCC)
R-Value Work:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts.

Nadal, M., Anton, R., Dorca-Arevalo, J., Estebanez-Perpina, E., Tizzano, E.F., Fuentes-Prior, P.

(2023) Protein Sci 32: e4553-e4553

PubMed: 36560896 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.4553
Primary Citation Related Structures:
7Z89, 7Z8A, 7Z9A, 7Z9B, 7ZAB, 7ZAC, 7ZAF, 7ZAM

PubMed Abstract:
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by the absence of a functional copy of the Survival of Motor Neuron 1 gene (SMN1). The nearly identical paralog, SMN2, cannot compensate for the loss of SMN1 because exon 7 is aberrantly skipped from most SMN2 transcripts, a process mediated by synergistic activities of Src-associated during mitosis, 68 kDa (Sam68/KHDRBS1) and heterogeneous nuclear ribonucleoprotein (hnRNP) A1. This results in the production of a truncated, nonfunctional protein that is rapidly degraded. Here, we present several crystal structures of Sam68 RNA-binding domain (RBD). Sam68-RBD forms stable symmetric homodimers by antiparallel association of helices α3 from two monomers. However, the details of domain organization and the dimerization interface differ significantly from previously characterized homologs. We demonstrate that Sam68 and hnRNP A1 can simultaneously bind proximal motifs within the central region of SMN2 (ex7). Furthermore, we show that the RNA-binding pockets of the two proteins are close to each other in their heterodimeric complex and identify contact residues using crosslinking-mass spectrometry. We present a model of the ternary Sam68·SMN2 (ex7)·hnRNP A1 complex that reconciles all available information on SMN1/2 splicing. Our findings have important implications for the etiology of SMA and open new avenues for the design of novel therapeutics to treat splicing diseases.

Organizational Affiliation

Molecular Bases of Disease, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.

Macromolecule Content

Total Structure Weight: 28.45 kDa
Atom Count: 1,991
Modeled Residue Count: 236
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1	A [auth AAA], B [auth BBB]	118	Homo sapiens	Mutation(s): 1 Gene Names: KHDRBS1, SAM68
UniProt & NIH Common Fund Data Resources
Find proteins for Q07666 (Homo sapiens) Explore Q07666 Go to UniProtKB: Q07666
PHAROS: Q07666 GTEx: ENSG00000121774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07666
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain O [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain O [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain O [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], O [auth BBB]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth AAA] Focus chain O [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain O [auth BBB]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth BBB] SDF format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain P [auth BBB]	P [auth BBB], Q [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth BBB] Focus chain Q [auth BBB] Interactions & Density Focus chain P [auth BBB] Focus chain Q [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth AAA] MOL2 format, chain N [auth AAA] mmCIF format, chain N [auth AAA]	N [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth AAA] Interactions & Density Focus chain N [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth BBB] SDF format, chain U [auth BBB] SDF format, chain T [auth BBB] SDF format, chain S [auth BBB] SDF format, chain R [auth BBB] SDF format, chain M [auth AAA] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain V [auth BBB] MOL2 format, chain U [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain V [auth BBB] mmCIF format, chain U [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA], R [auth BBB], S [auth BBB], T [auth BBB], U [auth BBB], V [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain V [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Focus chain V [auth BBB]