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- PDB-1mr1: Crystal Structure of a Smad4-Ski Complex -

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Basic information

Entry
Database: PDB / ID: 1mr1
TitleCrystal Structure of a Smad4-Ski Complex
Components
  • Mothers against decapentaplegic homolog 4
  • Ski oncogene
KeywordsSIGNALING PROTEIN / Smad / Ski / cancer / TGF-b signaling / protein interaction
Function / homology
Function and homology information


nose morphogenesis / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / histone deacetylase inhibitor activity / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / activin responsive factor complex / atrioventricular valve formation ...nose morphogenesis / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / histone deacetylase inhibitor activity / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / activin responsive factor complex / atrioventricular valve formation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / mesendoderm development / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / RUNX2 regulates bone development / heteromeric SMAD protein complex / epithelial cell migration / regulation of transforming growth factor beta2 production / positive regulation of follicle-stimulating hormone secretion / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / myotube differentiation / neuron fate specification / FOXO-mediated transcription of cell cycle genes / response to transforming growth factor beta / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / positive regulation of extracellular matrix assembly / negative regulation of cardiac muscle hypertrophy / atrioventricular canal development / Transcriptional regulation of pluripotent stem cells / cardiac conduction system development / camera-type eye morphogenesis / sulfate binding / Germ layer formation at gastrulation / olfactory bulb development / cellular response to BMP stimulus / SMAD protein signal transduction / Signaling by BMP / Formation of definitive endoderm / Signaling by Activin / myelination in peripheral nervous system / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / Signaling by NODAL / camera-type eye development / outflow tract septum morphogenesis / gastrulation with mouth forming second / I-SMAD binding / cardiac muscle hypertrophy in response to stress / bone morphogenesis / TGFBR3 expression / embryonic limb morphogenesis / Cardiogenesis / anterior/posterior axis specification / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / face morphogenesis / positive regulation of DNA binding / adrenal gland development / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / negative regulation of SMAD protein signal transduction / uterus development / TGF-beta receptor signaling activates SMADs / roof of mouth development / R-SMAD binding / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / somatic stem cell population maintenance / anatomical structure morphogenesis / developmental growth / negative regulation of BMP signaling pathway / positive regulation of Wnt signaling pathway / cardiac muscle cell proliferation / negative regulation of osteoblast differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / single fertilization / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / ovarian follicle development
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 ...: / 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
Ski oncogene / Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWu, J.-W. / Krawitz, A.R. / Chai, J. / Li, W. / Zhang, F. / Luo, K. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural Mechanism of Smad4 Recognition by the Nuclear Oncoprotein Ski: Insights on Ski-mediated Repression of TGF-beta Signaling
Authors: Wu, J.-W. / Krawitz, A.R. / Chai, J. / Li, W. / Zhang, F. / Luo, K. / Shi, Y.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: Mothers against decapentaplegic homolog 4
C: Ski oncogene
D: Ski oncogene
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4546
Polymers74,3234
Non-polymers1312
Water28816
1
A: Mothers against decapentaplegic homolog 4
D: Ski oncogene
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2273
Polymers37,1612
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area15090 Å2
MethodPISA
2
B: Mothers against decapentaplegic homolog 4
C: Ski oncogene
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2273
Polymers37,1612
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.8, 109.8, 141.1
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mothers against decapentaplegic homolog 4 / Smad4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / hSMAD4


Mass: 25642.287 Da / Num. of mol.: 2 / Fragment: MH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: Protein Ski oncogene / Ski / C-ski


Mass: 11519.203 Da / Num. of mol.: 2 / Fragment: Smad4-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12755
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
310 %(v/v)1,4-dioxane1reservoir
4900 mM1reservoirpH7.0K2HPO4/KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 15, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→99 Å / Num. all: 23957 / Num. obs: 22639 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.85→2.95 Å / % possible all: 61
Reflection
*PLUS
Lowest resolution: 99 Å / Redundancy: 6.1 % / Num. measured all: 136326 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 61.2 % / Rmerge(I) obs: 0.457

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→20 Å / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 998 random
Rwork0.231 --
all0.235 23446 -
obs0.235 20599 -
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 2 16 4684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.578
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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