5C4V | pdb_00005c4v

Ski-like protein

PDB DOI: https://doi.org/10.2210/pdb5C4V/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-18 Released: 2016-10-12
Deposition Author(s): Wallden, K., Nyman, T., Hallberg, B.M.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.242 (Depositor), 0.226 (DCC)
R-Value Work:
0.208 (Depositor), 0.191 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex.

Wallden, K., Nyman, T., Hallberg, B.M.

(2017) Sci Rep 7: 46370-46370

PubMed: 28397834 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep46370
Primary Citation Related Structures:
5C4V

PubMed Abstract:
TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.

Organizational Affiliation

Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 129.14 kDa
Atom Count: 6,835
Modeled Residue Count: 856
Deposited Residue Count: 1,155
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 4	A, B [auth C], C [auth E]	258	Homo sapiens	Mutation(s): 0 Gene Names: SMAD4, DPC4, MADH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens) Explore Q13485 Go to UniProtKB: Q13485
PHAROS: Q13485 GTEx: ENSG00000141646
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13485
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ski-like protein	D [auth B], E [auth D], F	127	Homo sapiens	Mutation(s): 0 Gene Names: SKIL, SNO
UniProt & NIH Common Fund Data Resources
Find proteins for P12757 (Homo sapiens) Explore P12757 Go to UniProtKB: P12757
PHAROS: P12757 GTEx: ENSG00000136603
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12757
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth D] SDF format, chain H [auth B] MOL2 format, chain L [auth F] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] mmCIF format, chain L [auth F] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B]	H [auth B], K [auth D], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth F] Interactions & Density Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth F]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.242 (Depositor), 0.226 (DCC)
R-Value Work: 0.208 (Depositor), 0.191 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.54	α = 90
b = 122.83	β = 90.72
c = 51.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Wallden, K.

Nyman, T.

Hallberg, B.M.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2017-04-19
Changes: Database references
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary