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- PDB-6zmn: Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to ... -

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Basic information

Entry
Database: PDB / ID: 6zmn
TitleCrystal structure of the Smad3-Smad5 MH1 domain chimera 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
KeywordsSIGNALING PROTEIN / Smad3 / transcription / TGFbeta / dimerization / hinge loop / protein engineering
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 / sterol response element binding / transdifferentiation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / transdifferentiation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex / negative regulation of osteoblast proliferation / 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 / FOXO-mediated transcription of cell cycle genes / bHLH transcription factor binding / trophoblast cell migration / negative regulation of transforming growth factor beta production / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / positive regulation of extracellular matrix assembly / negative regulation of wound healing / nuclear glucocorticoid receptor binding / Germ layer formation at gastrulation / primary miRNA processing / cell-cell junction organization / SMAD protein signal transduction / negative regulation of lipopolysaccharide-mediated signaling pathway / transforming growth factor beta receptor binding / Formation of definitive endoderm / signal transduction involved in regulation of gene expression / response to angiotensin / Signaling by Activin / activin receptor signaling pathway / negative regulation of ossification / Formation of axial mesoderm / ureteric bud development / Signaling by NODAL / regulation of dendritic spine morphogenesis / response to alcohol / Interleukin-37 signaling / adrenal gland development / I-SMAD binding / TGFBR3 expression / positive regulation of positive chemotaxis / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / negative regulation of fat cell differentiation / DNA-binding transcription repressor activity / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of bone mineralization / negative regulation of cytosolic calcium ion concentration / R-SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / positive regulation of focal adhesion assembly / cellular response to platelet-derived growth factor stimulus / cellular response to transforming growth factor beta stimulus / regulation of immune response / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / JNK cascade / anatomical structure morphogenesis / positive regulation of stress fiber assembly / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / phosphatase binding / cis-regulatory region sequence-specific DNA binding / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / response to gamma radiation / negative regulation of miRNA transcription / apoptotic signaling pathway / regulation of mitochondrial membrane potential / nuclear receptor binding / transcription corepressor binding / wound healing / positive regulation of interleukin-1 beta production / T cell activation / Downregulation of TGF-beta receptor signaling / cellular response to glucose stimulus / response to cocaine / cellular response to virus / ubiquitin binding / negative regulation of protein catabolic process / positive regulation of protein import into nucleus / promoter-specific chromatin binding / negative regulation of inflammatory response / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of cell growth / protein-DNA complex / chromatin DNA binding / positive regulation of miRNA transcription
Similarity search - Function
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 ...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
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / SMAD family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.333 Å
AuthorsPluta, R. / Macias, M.J.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-53787-P Spain
European Commission754510European Union
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes.
Authors: Ruiz, L. / Kaczmarska, Z. / Gomes, T. / Aragon, E. / Torner, C. / Freier, R. / Baginski, B. / Martin-Malpartida, P. / de Martin Garrido, N. / Marquez, J.A. / Cordeiro, T.N. / Pluta, R. / Macias, M.J.
History
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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)39,5499
Polymers39,1474
Non-polymers4025
Water28816
1
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

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')


Theoretical massNumber of molelcules
Total (without water)49,34911
Polymers48,9476
Non-polymers4025
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Unit cell
Length a, b, c (Å)54.502, 73.416, 111.154
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

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


Mass: 14673.113 Da / Num. of mol.: 2
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*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)

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Non-polymers , 5 types, 21 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: 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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Details

Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.37→48.94 Å / Num. obs: 12973 / % possible obs: 91.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 8.9
Reflection shellResolution: 2.37→2.64 Å / Redundancy: 2.9 % / Num. unique obs: 649 / CC1/2: 0.552 / Rpim(I) all: 0.531 / % possible all: 57.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5od6

5od6


Resolution: 2.333→26 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.853 / SU R Cruickshank DPI: 0.602 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.649 / SU Rfree Blow DPI: 0.304 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.252 650 -RANDOM
Rwork0.2099 ---
obs0.212 12963 66.1 %-
Displacement parametersBiso mean: 52.12 Å2
Baniso -1Baniso -2Baniso -3
1--11.8669 Å20 Å20 Å2
2--4.6495 Å20 Å2
3---7.2174 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.333→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 656 20 16 2670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913865HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d909SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes365HARMONIC5
X-RAY DIFFRACTIONt_it2773HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1646SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion22.38
LS refinement shellResolution: 2.333→3 Å
RfactorNum. reflection% reflection
Rfree0.293 16 -
Rwork0.2238 --
obs--8.19 %
Refinement TLS params.

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)
10.9345-0.1833-1.30610.26540.2362.16340.02110.2835-0.14760.2835-0.00070.0675-0.14760.0675-0.02040.10050.0354-0.07240.04160.053-0.003314.285228.2644-17.8534
20.40970.9208-0.96820.60580.27273.5632-0.2724-0.1135-0.186-0.11350.45370.2347-0.1860.2347-0.1813-0.0069-0.02180.01340.0277-0.07330.207930.914222.5339-45.1951
32.0895-1.7876-5.269311.0596-1.54328.8895-0.0126-0.35180.1435-0.3518-0.1142-0.07190.1435-0.07190.1268-0.4499-0.1392-0.1892-0.35960.0717-0.233218.24356.1166-13.1325
46.24740.9753-7.032512.8462-6.55362.5774-0.0495-0.3528-0.4988-0.35280.1509-0.1717-0.4988-0.1717-0.1014-0.4084-0.056-0.1706-0.2811-0.1387-0.164317.79548.5331-13.7844
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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