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- PDB-6tbz: Crystal structure of the MH1 domain of Smad5-Smad3 chimera constr... -

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Basic information

Entry
Database: PDB / ID: 6tbz
TitleCrystal structure of the MH1 domain of Smad5-Smad3 chimera construct 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 / TGF-B
Function / homology
Function and homology information


Signaling by BMP / : / 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 ...Signaling by BMP / : / 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 / transcription factor binding / cellular response to organic cyclic compound / anatomical structure morphogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / cardiac muscle contraction / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / bone development / DNA-binding transcription repressor activity, RNA polymerase II-specific / osteoblast differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / protein phosphorylation / 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 / cytoplasm / cytosol
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 / Mothers against decapentaplegic homolog 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsPluta, R. / Macias, M.J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
European Commission
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
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Apr 29, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 10, 2021Group: Database references / Refinement description / Category: citation / citation_author / software
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 / _citation_author.name / _software.name
Revision 1.4Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 5
B: DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')
C: 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)24,8984
Polymers24,8333
Non-polymers651
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.145, 53.145, 83.154
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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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: 15032.509 Da / Num. of mol.: 1
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, UniProt: Q56I99*PLUS
#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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.95 % / Description: elongated crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22% PEG 3350, 0.05 M sodium citrate pH 5.5

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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: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.78→46 Å / Num. obs: 11400 / % possible obs: 88.8 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.038 / Rrim(I) all: 0.087 / Net I/σ(I): 10.9
Reflection shellResolution: 1.82→2.08 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 571 / CC1/2: 0.578 / Rrim(I) all: 0.885 / % possible all: 68.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fzs

6fzs


Resolution: 1.782→46 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.287 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 550 -RANDOM
Rwork0.1916 ---
obs0.1932 11400 45.4 %-
Displacement parametersBiso mean: 63.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.111 Å20 Å20 Å2
2--4.111 Å20 Å2
3----8.222 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.782→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 656 1 57 1741
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081850HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.922643HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d576SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes222HARMONIC5
X-RAY DIFFRACTIONt_it1850HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1033SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion25.4
LS refinement shellResolution: 1.782→2 Å
RfactorNum. reflection% reflection
Rfree0.3566 22 -
Rwork0.2118 --
obs--5.06 %
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)
14.7332-0.0648-0.33363.6407-0.65346.49680.10930.14650.1830.1465-0.06190.33580.1830.3358-0.0474-0.06030.00660.01570.0560.0162-0.23717.26784.19536.4289
25.33151.69031.785910.1010.39395.9868-0.1513-0.1752-0.1407-0.17520.3309-0.0015-0.1407-0.0015-0.1797-0.3445-0.03740.0855-0.05290.15590.105311.650626.10932.058
34.45733.77272.49986.8208-0.33795.224-0.17970.0628-0.04230.06280.32750.0186-0.04230.0186-0.1478-0.39330.02530.1041-0.07150.12370.30410.914423.9912.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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