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- PDB-5od6: Crystal structure of Smad3-MH1 bound to the GGCGC site. -

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Basic information

Entry
Database: PDB / ID: 5od6
TitleCrystal structure of Smad3-MH1 bound to the GGCGC site.
Components
  • DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')
  • Mothers against decapentaplegic homolog 3
KeywordsTRANSCRIPTION / Smads / transcription factor / DNA complex
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / sterol response element binding / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / transdifferentiation / sterol response element binding / paraxial mesoderm morphogenesis / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / regulation of striated muscle tissue development / SMAD protein complex / immune system development / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / DEAD/H-box RNA helicase binding / bHLH transcription factor binding / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / negative regulation of wound healing / lens fiber cell differentiation / nuclear glucocorticoid receptor binding / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / endoderm development / signal transduction involved in regulation of gene expression / Formation of definitive endoderm / embryonic pattern specification / activin receptor signaling pathway / Signaling by Activin / cell-cell junction organization / Formation of axial mesoderm / SMAD protein signal transduction / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of cardiac muscle hypertrophy in response to stress / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / ureteric bud development / negative regulation of fat cell differentiation / DNA-binding transcription repressor activity / adrenal gland development / negative regulation of cytosolic calcium ion concentration / heart looping / TGF-beta receptor signaling activates SMADs / positive regulation of focal adhesion assembly / R-SMAD binding / thyroid gland development / mesoderm formation / developmental growth / anatomical structure morphogenesis / positive regulation of epithelial to mesenchymal transition / regulation of immune response / phosphatase binding / negative regulation of osteoblast differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / positive regulation of bone mineralization / somitogenesis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / JNK cascade / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / collagen binding / T cell activation / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / negative regulation of miRNA transcription / liver development / ubiquitin binding / positive regulation of interleukin-1 beta production / promoter-specific chromatin binding / nuclear receptor binding / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / wound healing / transcription coactivator binding / negative regulation of protein catabolic process / negative regulation of cell growth / chromatin DNA binding
Similarity search - Function
Smad3; Chain A / SMAD MH1 domain / 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 ...Smad3; Chain A / SMAD MH1 domain / 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 / SMAD/FHA domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaczmarska, Z. / Marquez, J.A. / Macias, M.J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.
Authors: Martin-Malpartida, P. / Batet, M. / Kaczmarska, Z. / Freier, R. / Gomes, T. / Aragon, E. / Zou, Y. / Wang, Q. / Xi, Q. / Ruiz, L. / Vea, A. / Marquez, J.A. / Massague, J. / Macias, M.J.
History
DepositionJul 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 3
B: Mothers against decapentaplegic homolog 3
C: DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')
D: DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0046
Polymers39,8744
Non-polymers1312
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomeric, gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 105.200, 73.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11D-111-

HOH

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Components

#1: Protein Mothers against decapentaplegic homolog 3 / / hMAD-3 / JV15-2 / SMAD family member 3 / hSMAD3


Mass: 15036.612 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GAMIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVETPVL
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3, MADH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#2: DNA chain DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')


Mass: 4900.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 26771 / % possible obs: 99.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 48.92 Å2 / Net I/σ(I): 7.51
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1917 / Rrim(I) all: 1.119 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ozj

1ozj


Resolution: 2→27.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1318 4.92 %RANDOM
Rwork0.195 ---
obs0.197 26771 98.9 %-
Displacement parametersBiso mean: 61.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.2463 Å20 Å20 Å2
2---3.2463 Å20 Å2
3---6.4926 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 656 2 167 2859
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012814HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13935HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d911SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it2814HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion19.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3041SEMIHARMONIC4
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.228 127 4.17 %
Rwork0.215 2916 -
all0.216 3043 -
obs--99.48 %
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)
12.2146-0.26580.32491.34720.4582.6716-0.0217-0.0162-0.09270.0497-0.0530.10810.3235-0.1240.0747-0.0399-0.00360.0646-0.08330.0373-0.0722135.7877.289212.4902
23.5755-0.29680.5025.01122.24315.8874-0.1370.07810.11160.1846-0.1043-0.0872-0.3320.21560.2413-0.12540.0319-0.039-0.15780.0632-0.1763161.73822.321624.7771
36.68584.21891.56026.1781-0.03726.2599-0.195-0.13720.3590.22990.10450.41720.3132-0.35320.0905-0.21050.050.0732-0.12050.0163-0.2539131.4891.0453-7.4582
44.6188-0.56544.67387.94140.07857.4539-0.21330.3545-0.0541-0.29260.07030.18850.4515-0.4380.143-0.2262-0.03910.0534-0.1332-0.0202-0.3145131.2890.359-9.7831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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