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- PDB-5xod: Crystal structure of human Smad2-Ski complex -

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Basic information

Entry
Database: PDB / ID: 5xod
TitleCrystal structure of human Smad2-Ski complex
Components
  • Mothers against decapentaplegic homolog 2
  • Ski oncogene
KeywordsTRANSCRIPTION / transcription factor / complex
Function / homology
Function and homology information


nose morphogenesis / zygotic specification of dorsal/ventral axis / histone deacetylase inhibitor activity / homomeric SMAD protein complex / activin responsive factor complex / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex ...nose morphogenesis / zygotic specification of dorsal/ventral axis / histone deacetylase inhibitor activity / homomeric SMAD protein complex / activin responsive factor complex / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / heteromeric SMAD protein complex / pericardium development / co-SMAD binding / myotube differentiation / determination of left/right asymmetry in lateral mesoderm / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / secondary palate development / trophoblast cell migration / odontoblast differentiation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / embryonic foregut morphogenesis / camera-type eye morphogenesis / Germ layer formation at gastrulation / primary miRNA processing / transforming growth factor beta receptor binding / olfactory bulb development / pulmonary valve morphogenesis / SMAD protein signal transduction / Signaling by BMP / Formation of definitive endoderm / type I transforming growth factor beta receptor binding / Signaling by Activin / embryonic cranial skeleton morphogenesis / myelination in peripheral nervous system / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Signaling by NODAL / response to cholesterol / camera-type eye development / pancreas development / I-SMAD binding / bone morphogenesis / embryonic limb morphogenesis / negative regulation of ossification / aortic valve morphogenesis / anterior/posterior axis specification / face morphogenesis / anterior/posterior pattern specification / ureteric bud development / endocardial cushion morphogenesis / insulin secretion / positive regulation of DNA binding / organ growth / SMAD binding / negative regulation of SMAD protein signal transduction / TGF-beta receptor signaling activates SMADs / roof of mouth development / R-SMAD binding / mesoderm formation / somatic stem cell population maintenance / negative regulation of cell differentiation / anatomical structure morphogenesis / negative regulation of BMP signaling pathway / cell fate commitment / cardiac muscle cell proliferation / negative regulation of osteoblast differentiation / positive regulation of Wnt signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatase binding / response to glucose / positive regulation of epithelial to mesenchymal transition / negative regulation of fibroblast proliferation / cis-regulatory region sequence-specific DNA binding / skeletal muscle fiber development / gastrulation / transcription repressor complex / transforming growth factor beta receptor signaling pathway / lung development / Downregulation of TGF-beta receptor signaling / post-embryonic development / neural tube closure / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cell motility / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / tau protein binding / disordered domain specific binding / retina development in camera-type eye / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
: / 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 / Tumour Suppressor Smad4 - #10 / MAD homology, MH1 ...: / 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 / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ski oncogene / Mothers against decapentaplegic homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsMiyazono, K. / Moriwaki, S. / Ito, T. / Tanokura, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS KAKENHI15K14708 Japan
JSPS KAKENHI23228003 Japan
CitationJournal: Sci Signal / Year: 2018
Title: Hydrophobic patches on SMAD2 and SMAD3 determine selective binding to cofactors
Authors: Miyazono, K.I. / Moriwaki, S. / Ito, T. / Kurisaki, A. / Asashima, M. / Tanokura, M.
History
DepositionMay 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 2
B: Ski oncogene


Theoretical massNumber of molelcules
Total (without water)25,6292
Polymers25,6292
Non-polymers00
Water93752
1
A: Mothers against decapentaplegic homolog 2
B: Ski oncogene

A: Mothers against decapentaplegic homolog 2
B: Ski oncogene

A: Mothers against decapentaplegic homolog 2
B: Ski oncogene


Theoretical massNumber of molelcules
Total (without water)76,8876
Polymers76,8876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12120 Å2
ΔGint-63 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.840, 110.840, 110.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Mothers against decapentaplegic homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / hSMAD2


Mass: 22461.432 Da / Num. of mol.: 1 / Fragment: UNP residues 262-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2, MADH2, MADR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15796
#2: Protein/peptide Ski oncogene / Proto-oncogene c-Ski


Mass: 3167.418 Da / Num. of mol.: 1 / Fragment: UNP residues 15-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKI / Production host: Escherichia coli (E. coli) / References: UniProt: P12755
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate tri-hydrate pH 4.6 and 1.85 M sodium formate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: CCD / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45.25 Å / Num. obs: 37448 / % possible obs: 99.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 31.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.012 / Rrim(I) all: 0.037 / Net I/σ(I): 28 / Num. measured all: 180013 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.895.70.529657911550.4420.2420.5832.997.7
9.07-45.258.80.0216671900.9990.0070.02292.799.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJS

1mjs


Resolution: 1.851→45.25 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 28.16 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2542 1978 5.28 %
Rwork0.2316 35470 -
obs0.2328 37448 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.73 Å2 / Biso mean: 60.5615 Å2 / Biso min: 24.71 Å2
Refinement stepCycle: final / Resolution: 1.851→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 0 52 1738
Biso mean---48.35 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021726
X-RAY DIFFRACTIONf_angle_d0.5852341
X-RAY DIFFRACTIONf_chiral_restr0.042256
X-RAY DIFFRACTIONf_plane_restr0.004304
X-RAY DIFFRACTIONf_dihedral_angle_d11.4241026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8509-1.89720.34831420.34932496263898
1.8972-1.94850.34721600.314125082668100
1.9485-2.00590.30071000.315825742674100
2.0059-2.07060.27421820.300425072689100
2.0706-2.14460.34741500.302124942644100
2.1446-2.23050.31791000.297726282728100
2.2305-2.3320.31931520.294524952647100
2.332-2.45490.32091340.305225552689100
2.4549-2.60870.36311300.307525522682100
2.6087-2.81010.27581280.277325452673100
2.8101-3.09280.23091720.259625202692100
3.0928-3.54020.25141240.217625332657100
3.5402-4.45970.24391460.18625312677100
4.4597-45.26370.1931580.170325322690100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5017-0.4592-1.8683.81692.85777.3260.15961.55790.23030.0721-0.99210.6842-1.1817-0.96040.60830.4584-0.1641-0.14580.59840.08090.95963.57915.684330.5554
23.0047-0.31610.66493.57310.17964.20190.1311-0.1309-1.1919-0.33230.1961-0.32170.2160.0606-0.21610.2457-0.0359-0.04730.24150.0450.608332.034310.678427.7186
33.010.41862.04662.02770.39131.39650.4893-1.3428-1.0140.6187-0.2140.03590.6165-1.10490.35250.4809-0.4418-0.23251.21190.59031.026329.93296.395744.266
42.0260.7126-0.57671.60340.40160.58630.3779-1.8166-0.90640.3361-0.2984-0.02420.3268-0.11740.0380.3977-0.2824-0.09290.91730.30790.545820.867512.844942.2438
50.92680.50991.9363.48552.06294.3676-0.4412-0.0564-0.92020.561-0.34010.44460.5246-0.90420.45640.4902-0.3577-0.06640.95590.39711.11183.03384.453643.1696
61.3351-0.512-2.02576.64480.72983.07560.04690.3553-0.7586-0.1406-0.1616-0.10860.10910.05390.350.4556-0.2456-0.07210.66180.22780.87978.32034.769133.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 274 )A260 - 274
2X-RAY DIFFRACTION2chain 'A' and (resid 275 through 354 )A275 - 354
3X-RAY DIFFRACTION3chain 'A' and (resid 355 through 380 )A355 - 380
4X-RAY DIFFRACTION4chain 'A' and (resid 381 through 456 )A381 - 456
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 30 )B15 - 30
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 36 )B31 - 36

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