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- PDB-7cd1: Crystal structure of inhibitory Smad, Smad7 -

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Basic information

Entry
Database: PDB / ID: 7cd1
TitleCrystal structure of inhibitory Smad, Smad7
ComponentsMothers against decapentaplegic homolog 7
KeywordsSIGNALING PROTEIN / MH2 domain / Smad / TGF-BETA / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / Signaling by BMP / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of TGF-beta receptor signaling / negative regulation of T cell cytokine production / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation ...positive regulation of chondrocyte hypertrophy / negative regulation of T-helper 17 type immune response / negative regulation of chondrocyte proliferation / Signaling by BMP / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of TGF-beta receptor signaling / negative regulation of T cell cytokine production / heteromeric SMAD protein complex / regulation of ventricular cardiac muscle cell membrane depolarization / negative regulation of T-helper 17 cell differentiation / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cell-cell adhesion / activin receptor binding / response to laminar fluid shear stress / negative regulation of transcription by competitive promoter binding / regulation of epithelial to mesenchymal transition / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / negative regulation of peptidyl-threonine phosphorylation / Ub-specific processing proteases / negative regulation of activin receptor signaling pathway / protein-containing complex localization / negative regulation of peptidyl-serine phosphorylation / adherens junction assembly / I-SMAD binding / negative regulation of ossification / artery morphogenesis / ureteric bud development / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / negative regulation of SMAD protein signal transduction / negative regulation of BMP signaling pathway / anatomical structure morphogenesis / regulation of cardiac muscle contraction / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / cellular response to transforming growth factor beta stimulus / collagen binding / negative regulation of protein ubiquitination / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / fibrillar center / transcription corepressor activity / cell differentiation / protein stabilization / intracellular signal transduction / centrosome / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
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 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural basis for inhibitory effects of Smad7 on TGF-beta family signaling.
Authors: Murayama, K. / Kato-Murayama, M. / Itoh, Y. / Miyazono, K. / Miyazawa, K. / Shirouzu, M.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Mothers against decapentaplegic homolog 7
B: Mothers against decapentaplegic homolog 7
C: Mothers against decapentaplegic homolog 7
D: Mothers against decapentaplegic homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,89019
Polymers85,8734
Non-polymers1,01715
Water8,971498
1
A: Mothers against decapentaplegic homolog 7
C: Mothers against decapentaplegic homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,59412
Polymers42,9362
Non-polymers65810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-123 kcal/mol
Surface area17190 Å2
MethodPISA
2
B: Mothers against decapentaplegic homolog 7
D: Mothers against decapentaplegic homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2967
Polymers42,9362
Non-polymers3595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-72 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.205, 117.426, 163.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Mothers against decapentaplegic homolog 7 / Smad7


Mass: 21468.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad7, Madh7, Madh8 / Production host: Escherichia coli (E. coli) / References: UniProt: O35253
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Na Citrate, MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 71133 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.128 / Net I/σ(I): 19.38
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 7017 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHX

1khx


Resolution: 1.89→36.5 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1392 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1994 3592 5.05 %
Rwork0.1738 67499 -
obs0.1751 71091 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.48 Å2
Refinement stepCycle: LAST / Resolution: 1.89→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 47 498 6425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076200
X-RAY DIFFRACTIONf_angle_d0.88398436
X-RAY DIFFRACTIONf_chiral_restr0.0595865
X-RAY DIFFRACTIONf_plane_restr0.00541091
X-RAY DIFFRACTIONf_dihedral_angle_d16.18432262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.26771030.22992473X-RAY DIFFRACTION94.81
1.92-1.950.26411110.22042567X-RAY DIFFRACTION99.96
1.95-1.970.26661650.19472585X-RAY DIFFRACTION99.93
1.97-20.21431320.19822524X-RAY DIFFRACTION99.96
2-2.030.21451470.19132593X-RAY DIFFRACTION100
2.03-2.070.24151250.18642576X-RAY DIFFRACTION100
2.07-2.10.21981410.18312560X-RAY DIFFRACTION100
2.1-2.140.21281530.18642599X-RAY DIFFRACTION100
2.14-2.180.26161350.17932555X-RAY DIFFRACTION100
2.18-2.230.24241360.18792594X-RAY DIFFRACTION100
2.23-2.280.22391350.18332610X-RAY DIFFRACTION100
2.28-2.330.2071380.1862572X-RAY DIFFRACTION100
2.33-2.390.23031400.18152563X-RAY DIFFRACTION100
2.39-2.450.19991400.18422601X-RAY DIFFRACTION100
2.45-2.520.25051490.18952580X-RAY DIFFRACTION100
2.52-2.60.20091220.18122608X-RAY DIFFRACTION100
2.6-2.70.21941330.19052596X-RAY DIFFRACTION100
2.7-2.810.22821380.18262608X-RAY DIFFRACTION100
2.81-2.930.20011280.18692612X-RAY DIFFRACTION100
2.93-3.090.20611340.17842621X-RAY DIFFRACTION100
3.09-3.280.19191410.1632602X-RAY DIFFRACTION100
3.28-3.530.15731440.1512623X-RAY DIFFRACTION100
3.53-3.890.17651510.14722616X-RAY DIFFRACTION99.96
3.89-4.450.15221320.14432660X-RAY DIFFRACTION100
4.45-5.610.16381530.15032645X-RAY DIFFRACTION99.96
5.61-36.50.21341660.20142756X-RAY DIFFRACTION99.93

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