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- PDB-6fzs: Crystal structure of Smad5-MH1 bound to the GGCGC site. -

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Basic information

Entry
Database: PDB / ID: 6fzs
TitleCrystal structure of Smad5-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 5
KeywordsTRANSCRIPTION / Smads / transcription factor / DNA complex
Function / homology
Function and homology information


negative regulation of Fas signaling pathway / Mullerian duct regression / osteoblast fate commitment / SMAD protein complex / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / cardiac conduction system development / Signaling by BMP / embryonic pattern specification / SMAD protein signal transduction ...negative regulation of Fas signaling pathway / Mullerian duct regression / osteoblast fate commitment / SMAD protein complex / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / cardiac conduction system development / Signaling by BMP / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development / ureteric bud development / germ cell development / cellular response to organic cyclic compound / anatomical structure morphogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / cardiac muscle contraction / transforming growth factor beta receptor signaling pathway / erythrocyte differentiation / bone development / DNA-binding transcription repressor activity, RNA polymerase II-specific / osteoblast differentiation / sequence-specific double-stranded DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKaczmarska, Z. / Marquez, J.A. / Macias, M.J.
Funding support Germany, Spain, France, 4items
OrganizationGrant numberCountry
European ComissionEMBL_291772 Germany
European ComissionIRBPostPro2.0_600404 Spain
Ministry of Economy and CompetitivenessBFU2014-53787-P Spain
European Commission653706 France
CitationJournal: Computational and Structural Biotechnology Journal / 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. / Marquez, J.A. / Cordeiro, T.N. / Pluta, R. / Macias, M.J.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
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 / _software.name
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 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 5
B: Mothers against decapentaplegic homolog 5
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)40,1486
Polymers40,0184
Non-polymers1312
Water2,576143
1
A: Mothers against decapentaplegic homolog 5
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

B: Mothers against decapentaplegic homolog 5
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)49,9498
Polymers49,8186
Non-polymers1312
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)67.764, 73.374, 89.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mothers against decapentaplegic homolog 5 / Mothers against DPP homolog 5 / JV5-1 / SMAD family member 5 / hSmad5


Mass: 15108.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD5, MADH5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99717
#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


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaF, 0.1 M bis-tris propane pH 7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.31→53.96 Å / Num. obs: 16675 / % possible obs: 92.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 49.64 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.052 / Net I/σ(I): 11.4
Reflection shellResolution: 2.31→2.481 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 834 / CC1/2: 0.529 / Rpim(I) all: 0.555 / % possible all: 44.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMP

3kmp


Resolution: 2.31→29.77 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.381 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.241 766 4.6 %RANDOM
Rwork0.193 ---
obs0.195 16665 83 %-
Displacement parametersBiso mean: 57.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.8191 Å20 Å20 Å2
2---1.1333 Å20 Å2
3----1.6858 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.31→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 656 2 143 2811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012798HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013916HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d890SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes367HARMONIC5
X-RAY DIFFRACTIONt_it2798HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion19.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion346SEMIHARMONIC5
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_contact2755SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.47 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2787 -6.25 %
Rwork0.2317 660 -
all0.2347 704 -
obs--19.77 %
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)
11.7415-0.4544-1.47850.87470.00754.1587-0.0171-0.32180.01230.0530.02030.0837-0.02960.1024-0.0032-0.05730.0048-0.0049-0.1046-0.0709-0.03416.9895-6.2586-18.8186
23.8391-0.2635-1.17411.2377-0.86451.6218-0.0222-0.06-0.1750.04430.07130.20380.1569-0.2954-0.04920.0409-0.08430.0079-0.1056-0.0008-0.141727.7343-48.2959-5.9429
32.8124-0.6341-1.071714.5402-1.49574.6858-0.0613-0.1709-0.12110.08370.4748-0.6846-0.4956-0.245-0.4135-0.35-0.0994-0.0387-0.18060.0583-0.24219.4226-28.8806-8.8861
42.302-2.709-2.613513.3474-2.49276.4547-0.0778-0.52520.1627-0.22290.3503-0.2147-0.644-0.4135-0.2725-0.2336-0.0173-0.0354-0.3036-0.0184-0.339118.1487-26.5229-10.1145
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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