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- PDB-5mey: Crystal structure of Smad4-MH1 bound to the GGCGC site. -

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Basic information

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


: / 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 / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer ...: / 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 / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / mesendoderm development / 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 / heteromeric SMAD protein complex / epithelial cell migration / regulation of transforming growth factor beta2 production / positive regulation of follicle-stimulating hormone secretion / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / FOXO-mediated transcription of cell cycle genes / response to transforming growth factor beta / neuron fate specification / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / positive regulation of extracellular matrix assembly / negative regulation of cardiac muscle hypertrophy / 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 / Signaling by BMP / SMAD protein signal transduction / Formation of definitive endoderm / 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 / adrenal gland development / embryonic digit morphogenesis / neural crest cell differentiation / branching involved in ureteric bud morphogenesis / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / uterus development / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / developmental growth / anatomical structure morphogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / BMP signaling pathway / single fertilization / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / positive regulation of cardiac muscle cell apoptotic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / ovarian follicle development / collagen binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / axon guidance / transcription corepressor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to glucose stimulus / 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 / positive regulation of miRNA transcription / transcription coactivator binding / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / intracellular iron ion homeostasis
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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / citation_author
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 / _citation_author.name
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
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,43815
Polymers20,7562
Non-polymers68213
Water1,65792
1
A: MH1 domain of human Smad4
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules

A: MH1 domain of human Smad4
D: DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87630
Polymers41,5124
Non-polymers1,36426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area7350 Å2
ΔGint-203 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.170, 79.000, 90.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain , 2 types, 2 molecules AD

#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.: 1
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*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')


Mass: 5518.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 105 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 17% PEG 6000, 0.2 M NaCl, 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 PILATUS 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: 2.05→50 Å / Num. obs: 14710 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.27 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 17.72
Reflection shellResolution: 2.05→2.06 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.59 / Num. measured obs: 1329 / Num. unique all: 221 / CC1/2: 0.653 / Rrim(I) all: 1.183 / % 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: 2.05→29.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.238 738 5.02 %RANDOM
Rwork0.222 ---
obs0.223 14709 100 %-
Displacement parametersBiso mean: 49.65 Å2
Baniso -1Baniso -2Baniso -3
1--9.5788 Å20 Å20 Å2
2--9.7001 Å20 Å2
3----0.1213 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.05→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 369 28 92 1468
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091429HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12001HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d447SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes166HARMONIC5
X-RAY DIFFRACTIONt_it1429HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion20.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion183SEMIHARMONIC5
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_contact1576SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.27 143 4.75 %
Rwork0.246 2865 -
all0.247 3008 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -15.9256 Å / Origin y: -16.9063 Å / Origin z: 3.2349 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °
Refinement TLS groupSelection details: { A|* }

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