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- PDB-1g88: S4AFL3ARG515 MUTANT -

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Basic information

Entry
Database: PDB / ID: 1g88
TitleS4AFL3ARG515 MUTANT
ComponentsSMAD4Mothers against decapentaplegic homolog 4
KeywordsTRANSCRIPTION / transcriptional factor / L3 loop mutant
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 / 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 / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / positive regulation of follicle-stimulating hormone secretion / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / neuron fate specification / epithelial to mesenchymal transition involved in endocardial cushion formation / filamin binding / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / response to transforming growth factor beta / secondary palate development / FOXO-mediated transcription of cell cycle genes / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / atrioventricular canal development / cardiac conduction system development / positive regulation of extracellular matrix assembly / Germ layer formation at gastrulation / sulfate binding / Signaling by BMP / Formation of definitive endoderm / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / SMAD protein signal transduction / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / endothelial cell activation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / adrenal gland development / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / single fertilization / TGF-beta receptor signaling activates SMADs / R-SMAD binding / uterus development / positive regulation of SMAD protein signal transduction / developmental growth / anatomical structure morphogenesis / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ovarian follicle development / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / collagen binding / 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 ERK1 and ERK2 cascade / transcription coactivator binding / negative regulation of protein catabolic process / negative regulation of cell growth / osteoblast differentiation / positive regulation of miRNA transcription / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / in utero embryonic development / intracellular iron ion homeostasis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding
Similarity search - Function
Tumour Suppressor Smad4 - #10 / 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 ...Tumour Suppressor Smad4 - #10 / 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 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChako, B.M. / Qin, B. / Lam, S.S. / Correia, J.J. / Lin, K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The L3 loop and C-terminal phosphorylation jointly define Smad protein trimerization.
Authors: Chacko, B.M. / Qin, B. / Correia, J.J. / Lam, S.S. / de Caestecker, M.P. / Lin, K.
History
DepositionNov 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMAD4
B: SMAD4
C: SMAD4


Theoretical massNumber of molelcules
Total (without water)88,0453
Polymers88,0453
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-18 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.855, 140.855, 194.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein SMAD4 / Mothers against decapentaplegic homolog 4 / DPC4


Mass: 29348.332 Da / Num. of mol.: 3 / Fragment: SMAD4 ACTIVE FRAGMENT / Mutation: R515S / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13485

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES12
2250 mMlithium sulfate12
310 %(v/v)PEG400012

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 72845 / Num. obs: 19552 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5.5 / Redundancy: 3.72 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.5 / % possible all: 88
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. measured all: 72845
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 88 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40.5 Å / Data cutoff high absF: 191639.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 897 -RANDOM
Rwork0.203 ---
all0.19 19954 --
obs0.203 18416 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 0 0 5431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 3→3.19 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.276 2557 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rwork: 0.276

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