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- PDB-1dev: CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING D... -

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Basic information

Entry
Database: PDB / ID: 1dev
TitleCRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD-BINDING DOMAIN OF SARA
Components
  • MAD (mothers against decapentaplegic, Drosophila) homolog 2
  • Smad anchor for receptor activationZinc finger FYVE domain-containing protein 9
KeywordsSIGNALING PROTEIN / BETA SHEET / THREE-HELIX BUNDLE
Function / homology
Function and homology information


zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / 1-phosphatidylinositol binding ...zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / 1-phosphatidylinositol binding / endoderm formation / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm / odontoblast differentiation / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / pulmonary valve morphogenesis / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / activin receptor signaling pathway / signal transduction involved in regulation of gene expression / Signaling by Activin / SMAD protein signal transduction / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Signaling by NODAL / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / aortic valve morphogenesis / pancreas development / insulin secretion / anterior/posterior pattern specification / ureteric bud development / endocardial cushion morphogenesis / endosomal transport / organ growth / adrenal gland development / SMAD binding / TGF-beta receptor signaling activates SMADs / R-SMAD binding / mesoderm formation / anatomical structure morphogenesis / phosphatase binding / cell fate commitment / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / gastrulation / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / post-embryonic development / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / lung development / tau protein binding / endocytosis / disordered domain specific binding / early endosome membrane / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / early endosome / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / metal ion binding
Similarity search - Function
Smad Anchor For Receptor Activation; Chain B / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) ...Smad Anchor For Receptor Activation; Chain B / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / Tumour Suppressor Smad4 - #10 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / 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 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Zinc finger, FYVE/PHD-type / Few Secondary Structures / Irregular / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Zinc finger FYVE domain-containing protein 9 / Mothers against decapentaplegic homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsShi, Y. / Wu, G.
CitationJournal: Science / Year: 2000
Title: Structural basis of Smad2 recognition by the Smad anchor for receptor activation.
Authors: Wu, G. / Chen, Y.G. / Ozdamar, B. / Gyuricza, C.A. / Chong, P.A. / Wrana, J.L. / Massague, J. / Shi, Y.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAD (mothers against decapentaplegic, Drosophila) homolog 2
B: Smad anchor for receptor activation
C: MAD (mothers against decapentaplegic, Drosophila) homolog 2
D: Smad anchor for receptor activation


Theoretical massNumber of molelcules
Total (without water)52,8184
Polymers52,8184
Non-polymers00
Water0
1
A: MAD (mothers against decapentaplegic, Drosophila) homolog 2
B: Smad anchor for receptor activation


Theoretical massNumber of molelcules
Total (without water)26,4092
Polymers26,4092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area11000 Å2
MethodPISA
2
C: MAD (mothers against decapentaplegic, Drosophila) homolog 2
D: Smad anchor for receptor activation


Theoretical massNumber of molelcules
Total (without water)26,4092
Polymers26,4092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.5, 138.5, 55.9
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a hetero-dimer of Smad2 and SARA.

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Components

#1: Protein MAD (mothers against decapentaplegic, Drosophila) homolog 2


Mass: 22276.291 Da / Num. of mol.: 2 / Fragment: SMAD2 MH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: THIS SEQUENCE OCCURS NATURALLY IN HUMANS / Plasmid: PET3 AND PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q15796
#2: Protein/peptide Smad anchor for receptor activation / Zinc finger FYVE domain-containing protein 9


Mass: 4132.583 Da / Num. of mol.: 2 / Fragment: SARA SMAD2-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: THIS SEQUENCE OCCURS NATURALLY IN HUMANS / Plasmid: PET3 AND PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: O95405

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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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: TRIS, DIOXANE, AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
210 %(v/v)dioxane1reservoir
32.0 Mammonium sulfate1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.15
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 31596 / Num. obs: 31296 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 45
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.167 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 218815
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→20 Å / σ(F): 1.414 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1489 -5% OF REFLECTIONS, RANDOM CHOSEN
Rwork0.218 ---
all0.22 31596 --
obs0.22 31296 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 0 0 3645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.343
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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