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- PDB-5mf0: Crystal structure of Smad4-MH1 bound to the GGCCG site. -

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Basic information

Entry
Database: PDB / ID: 5mf0
TitleCrystal structure of Smad4-MH1 bound to the GGCCG site.
Components
  • DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')
  • MH1 domain of human Smad4
KeywordsTRANSCRIPTION / Smads / transcription factor / DNA complex
Function / homology
Function and homology information


positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / RUNX3 regulates BCL2L11 (BIM) transcription / mesendoderm development ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / RUNX3 regulates BCL2L11 (BIM) transcription / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / filamin binding / SMAD protein complex / positive regulation of luteinizing hormone secretion / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / regulation of transforming growth factor beta2 production / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / endocardial cell differentiation / neuron fate specification / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / negative regulation of cardiac muscle hypertrophy / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / outflow tract septum morphogenesis / positive regulation of extracellular matrix assembly / sulfate binding / Germ layer formation at gastrulation / cellular response to BMP stimulus / Signaling by BMP / Formation of definitive endoderm / activin receptor signaling pathway / SMAD protein signal transduction / Signaling by Activin / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / TGFBR3 expression / gastrulation with mouth forming second / I-SMAD binding / endothelial cell activation / neural crest cell differentiation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / adrenal gland development / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of cardiac muscle cell apoptotic process / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling activates SMADs / uterus development / R-SMAD binding / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / developmental growth / single fertilization / anatomical structure morphogenesis / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ovarian follicle development / cellular response to transforming growth factor beta stimulus / extrinsic apoptotic signaling pathway / collagen binding / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / axon guidance / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / transcription coactivator binding / positive regulation of miRNA transcription / osteoblast differentiation / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsKaczmarska, Z. / Freier, R. / 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
DepositionNov 16, 2016Deposition 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 1.2Jan 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: MH1 domain of human Smad4
B: MH1 domain of human Smad4
E: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4798
Polymers40,2774
Non-polymers2024
Water724
1
A: MH1 domain of human Smad4
E: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')
hetero molecules

B: MH1 domain of human Smad4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4798
Polymers40,2774
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_474y-1,-x+2,z-3/41
Buried area4130 Å2
ΔGint-56 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.520, 101.520, 45.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein MH1 domain of human Smad4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD family member 4 / hSMAD4


Mass: 15237.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, DPC4, MADH4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: DNA chain DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')


Mass: 4901.155 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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 16% PEG MME 2000 and 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.03→30 Å / Num. obs: 9289 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 97.46 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0116 / Net I/σ(I): 12.06
Reflection shellResolution: 3.03→3.04 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.76 / Num. measured obs: 436 / Num. unique all: 85 / CC1/2: 0.721 / Rrim(I) all: 0.981 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qsv

3qsv


Resolution: 3.03→28.25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.891 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.425
RfactorNum. reflection% reflectionSelection details
Rfree0.27 432 4.65 %RANDOM
Rwork0.231 ---
obs0.232 9289 99.9 %-
Displacement parametersBiso mean: 73.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.8749 Å20 Å20 Å2
2--2.8749 Å20 Å2
3----5.7497 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: 1 / Resolution: 3.03→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 656 4 4 2604
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082718HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973821HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d835SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it2718HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion23.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion354SEMIHARMONIC5
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_contact2775SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.384 133 5.11 %
Rwork0.311 2470 -
all0.315 2603 -
obs--99.92 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
115.0102132.61348.253
231.4844116.44961.7762
322.2016154.23237.9675
422.8261152.55739.9363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ E|* }
4X-RAY DIFFRACTION4{ F|* }

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