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- PDB-5mez: Crystal structure of Smad4-MH1 bound to the GGCT site. -

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Basic information

Entry
Database: PDB / ID: 5mez
TitleCrystal structure of Smad4-MH1 bound to the GGCT site.
Components
  • DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-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 / activin responsive factor complex / atrioventricular valve formation / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...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 / activin responsive factor complex / atrioventricular valve formation / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / neuron fate specification / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / negative regulation of cardiac muscle hypertrophy / positive regulation of extracellular matrix assembly / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / sulfate binding / Germ layer formation at gastrulation / cellular response to BMP stimulus / Formation of definitive endoderm / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / outflow tract septum morphogenesis / gastrulation with mouth forming second / I-SMAD binding / cardiac muscle hypertrophy in response to stress / TGFBR3 expression / Cardiogenesis / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / embryonic digit morphogenesis / adrenal gland development / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / uterus development / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / developmental growth / epithelial to mesenchymal transition / anatomical structure morphogenesis / BMP signaling pathway / single fertilization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of cardiac muscle cell apoptotic process / ovarian follicle development / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / axon guidance / transcription corepressor binding / 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 / transcription coactivator binding / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / positive regulation of miRNA transcription / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / transcription by RNA polymerase II
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: 2.98 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

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Assembly

Deposited unit
A: MH1 domain of human Smad4
B: MH1 domain of human Smad4
D: DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
E: DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4407
Polymers40,2744
Non-polymers1663
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-34 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 79.060, 114.160
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 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*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')


Mass: 4899.179 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.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3350, 0.2 M calcium chloride

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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: Aug 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.98→30 Å / Num. obs: 12239 / % possible obs: 99.7 % / Redundancy: 3.83 % / Biso Wilson estimate: 90.22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.094 / Net I/σ(I): 12.86
Reflection shellResolution: 2.98→2.99 Å / Redundancy: 4.06 % / Mean I/σ(I) obs: 1.68 / Num. measured obs: 459 / Num. unique all: 113 / CC1/2: 0.699 / Rrim(I) all: 0.915 / % possible all: 100

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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: 2.98→29.05 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.888 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.705 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.775 / SU Rfree Blow DPI: 0.343 / SU Rfree Cruickshank DPI: 0.341
RfactorNum. reflection% reflectionSelection details
Rfree0.252 580 4.74 %RANDOM
Rwork0.217 ---
obs0.218 12239 98 %-
Displacement parametersBiso mean: 80.41 Å2
Baniso -1Baniso -2Baniso -3
1--12.7528 Å20 Å20 Å2
2---6.7068 Å20 Å2
3---19.4596 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: 1 / Resolution: 2.98→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 616 3 7 2530
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012639HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053707HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d802SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2639HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion20.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion347SEMIHARMONIC5
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_contact2722SEMIHARMONIC4
LS refinement shellResolution: 2.98→3.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 144 4.93 %
Rwork0.262 2776 -
all0.264 2920 -
obs--99.69 %
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)
113.163110.793217.7533
216.3081-1.80444.4585
330.89726.191416.0827
430.943922.705516.1406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }

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