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- PDB-5odg: Crystal structure of Smad3-MH1 bound to the GGCT site. -

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Basic information

Entry
Database: PDB / ID: 5odg
TitleCrystal structure of Smad3-MH1 bound to the GGCT site.
Components
  • DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*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 / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / primary miRNA processing / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / nuclear glucocorticoid receptor binding / endoderm development / Formation of definitive endoderm / embryonic pattern specification / signal transduction involved in regulation of gene expression / activin receptor signaling pathway / Signaling by Activin / SMAD protein signal transduction / Formation of axial mesoderm / cell-cell junction organization / 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 / DNA-binding transcription repressor activity / adrenal gland development / negative regulation of fat cell differentiation / 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 / regulation of immune response / phosphatase binding / negative regulation of osteoblast differentiation / anatomical structure morphogenesis / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of bone mineralization / somitogenesis / positive regulation of epithelial to mesenchymal transition / 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 / positive regulation of interleukin-1 beta production / ubiquitin binding / 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 / negative regulation of protein catabolic process / negative regulation of cell growth / chromatin DNA binding / cellular response to virus
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 / Resolution: 2.12 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 5, 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 1.2May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 3
B: Mothers against decapentaplegic homolog 3
D: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
E: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0387
Polymers39,8724
Non-polymers1663
Water1,45981
1
A: Mothers against decapentaplegic homolog 3
D: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
E: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
hetero molecules

B: Mothers against decapentaplegic homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0387
Polymers39,8724
Non-polymers1663
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-y+1/2,x,z+3/41
2
B: Mothers against decapentaplegic homolog 3
hetero molecules

A: Mothers against decapentaplegic homolog 3
D: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
E: DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0387
Polymers39,8724
Non-polymers1663
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554y,-x+1/2,z-3/41
Unit cell
Length a, b, c (Å)104.990, 104.990, 72.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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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 / Fragment: MH1 domain, UNP residues 11-135
Source method: isolated from a genetically manipulated source
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*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')


Mass: 4899.179 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium potassium phosphate, 0.1 M BisTris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. obs: 22058 / % possible obs: 99.9 % / Redundancy: 3.77 % / Biso Wilson estimate: 52.23 Å2 / Rrim(I) all: 0.049 / Net I/σ(I): 14.84
Reflection shellResolution: 2.12→2.13 Å / Redundancy: 3.64 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 292 / Rrim(I) all: 0.6635 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.12→29.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1075 4.87 %RANDOM
Rwork0.199 ---
obs0.202 22057 98.5 %-
Displacement parametersBiso mean: 66.48 Å2
Baniso -1Baniso -2Baniso -3
1--5.6349 Å20 Å20 Å2
2---5.6349 Å20 Å2
3---11.2697 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.12→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 533 3 81 2643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012668HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063712HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d875SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes319HARMONIC5
X-RAY DIFFRACTIONt_it2668HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion19.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion339SEMIHARMONIC5
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_contact2750SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.22 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.263 128 4.41 %
Rwork0.2288 2776 -
all0.2303 2904 -
obs--99.42 %
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)
11.8577-0.1622-0.48362.6262-0.70252.4706-0.0047-0.0482-0.1209-0.0062-0.03770.00510.2778-0.42760.0424-0.0139-0.0127-0.0413-0.0264-0.0707-0.1397.130730.8741-8.8997
24.9206-1.1159-1.34513.9036-0.02096.39020.01910.00640.2739-0.2504-0.0897-0.162-0.27420.40810.0706-0.110.0263-0.0758-0.12180.0084-0.189122.531556.4412-21.3275
34.09451.2005-1.54146.0982-1.01568.24650.04-0.0680.34610.5145-0.29630.16770.0092-0.49350.2563-0.1162-0.0861-0.0370.1565-0.0278-0.32831.026730.597512.2141
44.55452.03542.03328.0763-2.054310.48080.07830.24820.2182-0.1597-0.3628-0.1876-0.205-0.87350.2844-0.2550.06520.01080.1564-0.068-0.3128-0.132331.161510.2496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }

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