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- PDB-5c4v: Ski-like protein -

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Basic information

Entry
Database: PDB / ID: 5c4v
TitleSki-like protein
Components
  • Mothers against decapentaplegic homolog 4
  • Ski-like protein
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / lymphocyte homeostasis / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of follicle-stimulating hormone secretion / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / neuron fate specification / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / negative regulation of cardiac muscle hypertrophy / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / sulfate binding / Germ layer formation at gastrulation / cellular response to BMP stimulus / Formation of definitive endoderm / SMAD protein signal transduction / Signaling by BMP / response to growth factor / Signaling by Activin / outflow tract septum morphogenesis / activin receptor signaling pathway / Signaling by NODAL / blastocyst formation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / gastrulation with mouth forming second / I-SMAD binding / TGFBR3 expression / cardiac muscle hypertrophy in response to stress / positive regulation of axonogenesis / Cardiogenesis / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / adrenal gland development / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / uterus development / R-SMAD binding / TGF-beta receptor signaling activates SMADs / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of BMP signaling pathway / positive regulation of SMAD protein signal transduction / negative regulation of cell differentiation / single fertilization / anatomical structure morphogenesis / epithelial to mesenchymal transition / developmental growth / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / skeletal muscle tissue development / ovarian follicle development / positive regulation of cardiac muscle cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to transforming growth factor beta stimulus / collagen binding / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / response to cytokine / transforming growth factor beta receptor signaling pathway / axon guidance / acrosomal vesicle / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
SAND domain-like / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC Dachshund homology domain / SAND domain / Tumour Suppressor Smad4 - #10 ...SAND domain-like / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC Dachshund homology domain / SAND domain / Tumour Suppressor Smad4 - #10 / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / SAND-like domain superfamily / Tumour Suppressor Smad4 / Putative DNA-binding domain superfamily / SMAD/FHA domain superfamily / Roll / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Ski-like protein / Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWallden, K. / Nyman, T. / Hallberg, B.M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Sci Rep / Year: 2017
Title: SnoN Stabilizes the SMAD3/SMAD4 Protein Complex.
Authors: Wallden, K. / Nyman, T. / Hallberg, B.M.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
E: Mothers against decapentaplegic homolog 4
B: Ski-like protein
D: Ski-like protein
F: Ski-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14112
Polymers128,7366
Non-polymers4066
Water2,342130
1
A: Mothers against decapentaplegic homolog 4
B: Ski-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1876
Polymers42,9122
Non-polymers2754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Mothers against decapentaplegic homolog 4
D: Ski-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9773
Polymers42,9122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Mothers against decapentaplegic homolog 4
F: Ski-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9773
Polymers42,9122
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.540, 122.830, 51.570
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAHISHISAA319 - 54128 - 250
21ALAALAHISHISCB319 - 54128 - 250
12ALAALAHISHISAA319 - 54128 - 250
22ALAALAHISHISEC319 - 54128 - 250
13ALAALATHRTHRCB319 - 54228 - 251
23ALAALATHRTHREC319 - 54228 - 251
14PHEPHEMETMETBD262 - 35126 - 115
24PHEPHEMETMETDE262 - 35126 - 115
15PHEPHEGLUGLUBD262 - 35326 - 117
25PHEPHEGLUGLUFF262 - 35326 - 117
16PHEPHEMETMETDE262 - 35126 - 115
26PHEPHEMETMETFF262 - 35126 - 115

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Mothers against decapentaplegic homolog 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD family member 4 / hSMAD4


Mass: 28294.082 Da / Num. of mol.: 3 / Fragment: residues 314-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, DPC4, MADH4 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q13485
#2: Protein Ski-like protein / Ski-related oncogene / Ski-related protein


Mass: 14617.815 Da / Num. of mol.: 3 / Fragment: residues 238-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIL, SNO / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P12757

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Non-polymers , 4 types, 136 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.835
11-1/2H+3/2K, -1/2H-1/2K, L20.165
ReflectionResolution: 2.6→40.3 Å / Num. obs: 39718 / % possible obs: 97.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 42.5 Å2 / Net I/σ(I): 3.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 0.7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.6→40.3 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.877 / SU B: 5.86 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24212 1680 4.2 %RANDOM
Rwork0.20775 ---
obs0.20923 37935 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.514 Å2
Baniso -1Baniso -2Baniso -3
1--10.28 Å20 Å2-3.56 Å2
2---12.94 Å20 Å2
3---23.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6688 0 11 130 6829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196881
X-RAY DIFFRACTIONr_bond_other_d0.0090.026302
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9369335
X-RAY DIFFRACTIONr_angle_other_deg1.616314473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8865849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89723.229319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.666151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7151544
X-RAY DIFFRACTIONr_chiral_restr0.1050.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217842
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3684.0113417
X-RAY DIFFRACTIONr_mcbond_other4.364.013416
X-RAY DIFFRACTIONr_mcangle_it6.686.0044256
X-RAY DIFFRACTIONr_mcangle_other6.6816.0054257
X-RAY DIFFRACTIONr_scbond_it4.1484.1093464
X-RAY DIFFRACTIONr_scbond_other4.1484.1093464
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.296.0865079
X-RAY DIFFRACTIONr_long_range_B_refined10.92936.90827596
X-RAY DIFFRACTIONr_long_range_B_other10.92936.90827596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A217600.1
12C217600.1
21A217620.11
22E217620.11
31C219720.09
32E219720.09
41B81200.13
42D81200.13
51B72300.15
52F72300.15
61D69300.15
62F69300.15
LS refinement shellResolution: 2.572→2.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 58 -
Rwork0.349 1583 -
obs--53.28 %

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