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- PDB-1dd1: CRYSTAL STRUCTURE ANALYSIS OF THE SMAD4 ACTIVE FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1dd1
TitleCRYSTAL STRUCTURE ANALYSIS OF THE SMAD4 ACTIVE FRAGMENT
ComponentsSMAD4
KeywordsSIGNALING PROTEIN / B-SHEET SANDWICH HELIX-TURN-HELIX
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 / 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 / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / negative regulation of cardiac muscle hypertrophy / positive regulation of extracellular matrix assembly / 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 / outflow tract septum morphogenesis / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / I-SMAD binding / TGFBR3 expression / cardiac muscle hypertrophy in response to stress / Cardiogenesis / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / adrenal gland development / branching involved in ureteric bud morphogenesis / embryonic digit 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 / single fertilization / anatomical structure morphogenesis / epithelial to mesenchymal transition / developmental growth / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / ovarian follicle development / positive regulation of cardiac muscle cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to transforming growth factor beta stimulus / collagen binding / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / cellular response to glucose stimulus / transcription coactivator binding / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / 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
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 / Resolution: 2.62 Å
AuthorsQin, B.Y. / Lam, S.W. / Lin, K.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of a transcriptionally active Smad4 fragment.
Authors: Qin, B. / Lam, S.S. / Lin, K.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,12012
Polymers88,2553
Non-polymers8659
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-137 kcal/mol
Surface area31890 Å2
MethodPISA
2
A: SMAD4
B: SMAD4
C: SMAD4
hetero molecules

A: SMAD4
B: SMAD4
C: SMAD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,24024
Polymers176,5116
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area16700 Å2
ΔGint-294 kcal/mol
Surface area61400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.433, 142.433, 195.478
Angle α, β, γ (deg.)90, 90, 90
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-554-

SO4

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Components

#1: Protein SMAD4


Mass: 29418.445 Da / Num. of mol.: 3 / Fragment: SMAD4 ACTIVE FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13485
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN IS A COMMON MEDIATOR OF THE TGF-BETA SIGNALLING PATHWAY.

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, LISO4, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Temp details: ROOM
Crystal grow
*PLUS
Details: drop was combined with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
2100 mMHEPES1reservoir
310 %PEG40001reservoir
4200 mM1reservoirLi2SO4

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→100 Å / Num. all: 149316 / Num. obs: 29751 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.02 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.17
Reflection shellResolution: 2.62→2.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.02 / % possible all: 96.3
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.62→100 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE AND SIMULATED ANNEALING PROTOCOL
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1395 4.9 %RANDOM
Rwork0.218 ---
all0.218 28258 --
obs0.218 28258 92.9 %-
Refinement stepCycle: LAST / Resolution: 2.62→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 45 302 5890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.207
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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