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- PDB-6h3r: Crystal structure of Smad2 without exon -MH1 bound to the CAGAC site. -

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Basic information

Entry
Database: PDB / ID: 6h3r
TitleCrystal structure of Smad2 without exon -MH1 bound to the CAGAC site.
Components
  • DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
  • Mothers against decapentaplegic homolog
KeywordsTRANSCRIPTION / Smads / transcription factor / DNA complex
Function / homology
Function and homology information


transforming growth factor beta receptor signaling pathway / transcription regulator complex / membrane => GO:0016020 / regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKaczmarska, Z. / Marquez, J.A. / Macias, M.J.
Funding support Germany, Spain, France, 4items
OrganizationGrant numberCountry
European CommissionEMBL_291772 Germany
European CommissionIRBPostPro2.0_600404 Spain
Ministry of Economy and CompetitivenessBFU2014-53787-P Spain
European Commission653706 France
CitationJournal: Genes Dev. / Year: 2020
Title: Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-beta signaling
Authors: Aragon, E. / Wang, Q. / Zou, Y. / Morgani, S.M. / Ruiz, L. / Kaczmarska, Z. / Su, J. / Torner, C. / Tian, L. / Hu, J. / Shu, W. / Agrawal, S. / Gomes, T. / Marquez, J.A. / Hadjantonakis, A.- ...Authors: Aragon, E. / Wang, Q. / Zou, Y. / Morgani, S.M. / Ruiz, L. / Kaczmarska, Z. / Su, J. / Torner, C. / Tian, L. / Hu, J. / Shu, W. / Agrawal, S. / Gomes, T. / Marquez, J.A. / Hadjantonakis, A.-K. / Macias, M.J. / Massague, J.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _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
B: Mothers against decapentaplegic homolog
C: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
D: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5566
Polymers42,4254
Non-polymers1312
Water21612
1
B: Mothers against decapentaplegic homolog
hetero molecules

C: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
D: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,7954
Polymers26,7293
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-y+1/2,x+1/2,z-1/41
2
A: Mothers against decapentaplegic homolog
C: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
D: DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7954
Polymers26,7293
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.140, 80.140, 143.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Mothers against decapentaplegic homolog / Mothers against DPP homolog / SMAD family member


Mass: 15695.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2 / Production host: Escherichia coli (E. coli) / References: UniProt: B7Z5N5
#2: DNA chain DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')


Mass: 5516.578 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.: 12 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES 6.5 30% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 12777 / % possible obs: 99.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 116.42 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.092 / Net I/σ(I): 14.85
Reflection shellResolution: 2.75→2.76 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 154 / CC1/2: 0.62 / Rrim(I) all: 0.1266 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ozj

1ozj


Resolution: 2.75→27.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.612 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.73 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.276
RfactorNum. reflection% reflectionSelection details
Rfree0.222 650 5.09 %RANDOM
Rwork0.201 ---
obs0.202 12775 100 %-
Displacement parametersBiso mean: 92.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.8953 Å20 Å20 Å2
2--2.8953 Å20 Å2
3----5.7906 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.75→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 738 2 12 2661
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012779HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043916HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d852SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes356HARMONIC5
X-RAY DIFFRACTIONt_it2779HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion20.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion356SEMIHARMONIC5
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_contact2735SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.78 Å / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.2401 -5 %
Rwork0.3112 380 -
all0.3079 400 -
obs--100 %
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)
16.2742-1.5286-2.29883.0331-0.58458.64050.21730.38450.0374-0.3568-0.1880.15670.25860.6564-0.0293-0.08580.1862-0.05680.00570.0147-0.1476-16.51242.9946-15.8908
28.6530.1859-3.36474.8352.16187.77970.257-0.4686-0.07730.7298-0.6244-0.1743-0.3721-0.44770.3674-0.0853-0.1605-0.0456-0.1437-0.0407-0.091516.07187.2371-22.2809
37.6948-5.52710.242411.47621.15822.3791-0.28510.3284-0.57980.20330.11331.0885-0.04490.19660.1718-0.15270.1054-0.0614-0.21220.10420.039-33.95697.92930.0525
49.8761-5.13930.023210.14621.74473.5065-0.16870.1588-0.4668-0.16680.00011.08850.12510.08710.1685-0.1710.087-0.0769-0.19810.0633-0.0923-32.7916.6496-1.7721
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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