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- PDB-1mk2: SMAD3 SBD complex -

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Basic information

Entry
Database: PDB / ID: 1mk2
TitleSMAD3 SBD complex
Components
  • Madh-interacting protein
  • SMAD 3
KeywordsTRANSCRIPTION / SMAD3 / SBD / SARA
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / paraxial mesoderm morphogenesis / transdifferentiation / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / paraxial mesoderm morphogenesis / transdifferentiation / sterol response element binding / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / 1-phosphatidylinositol binding / immune system development / regulation of striated muscle tissue development / heteromeric SMAD protein complex / co-SMAD binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / FOXO-mediated transcription of cell cycle genes / DEAD/H-box RNA helicase binding / regulation of transforming growth factor beta receptor signaling pathway / pericardium development / negative regulation of osteoblast proliferation / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / nuclear glucocorticoid receptor binding / embryonic foregut morphogenesis / negative regulation of wound healing / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / primary miRNA processing / Formation of definitive endoderm / SMAD protein signal transduction / embryonic pattern specification / endoderm development / Signaling by Activin / activin receptor signaling pathway / Formation of axial mesoderm / cell-cell junction organization / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / Interleukin-37 signaling / TGFBR3 expression / response to angiotensin / nuclear inner membrane / signal transduction involved in regulation of gene expression / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of ossification / RUNX3 regulates CDKN1A transcription / endosomal transport / ureteric bud development / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cytosolic calcium ion concentration / DNA-binding transcription repressor activity / adrenal gland development / negative regulation of fat cell differentiation / heart looping / R-SMAD binding / TGF-beta receptor signaling activates SMADs / thyroid gland development / mesoderm formation / positive regulation of SMAD protein signal transduction / negative regulation of cell differentiation / positive regulation of focal adhesion assembly / anatomical structure morphogenesis / negative regulation of osteoblast differentiation / developmental growth / regulation of immune response / positive regulation of bone mineralization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / somitogenesis / phosphatase binding / positive regulation of epithelial to mesenchymal transition / cis-regulatory region sequence-specific DNA binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to transforming growth factor beta stimulus / collagen binding / extrinsic apoptotic signaling pathway / positive regulation of stress fiber assembly / JNK cascade / transforming growth factor beta receptor signaling pathway / negative regulation of miRNA transcription / release of cytochrome c from mitochondria / T cell activation / positive regulation of DNA-binding transcription factor activity / regulation of mitochondrial membrane potential / liver development / Downregulation of TGF-beta receptor signaling / ubiquitin binding / positive regulation of interleukin-1 beta production / transcription corepressor binding
Similarity search - Function
Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / Tumour Suppressor Smad4 - #10 / FYVE zinc finger ...Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / Tumour Suppressor Smad4 - #10 / FYVE zinc finger / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / FYVE zinc finger / MAD homology domain 1 (MH1) profile. / Protein present in Fab1, YOTB, Vac1, and EEA1 / 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 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Zinc finger FYVE domain-containing protein 9 / Mothers against decapentaplegic homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsQin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
CitationJournal: Genes Dev. / Year: 2002
Title: Smad3 allostery links TGF-beta receptor kinase activation to transcriptional control
Authors: Qin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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: SMAD 3
B: Madh-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2866
Polymers27,0462
Non-polymers2404
Water00
1
A: SMAD 3
B: Madh-interacting protein
hetero molecules

A: SMAD 3
B: Madh-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,57212
Polymers54,0914
Non-polymers4808
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area10940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.995, 71.716, 86.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis:

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Components

#1: Protein SMAD 3 / Mad3 / hMAD-3 / mMad3 / JV15-2 / hSMAD3


Mass: 23227.361 Da / Num. of mol.: 1 / Fragment: MH2 domain, residues 220-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#2: Protein/peptide Madh-interacting protein / Smad anchor for receptor activation / Receptor activation anchor / hSARA / Novel serine protease / NSP


Mass: 3818.246 Da / Num. of mol.: 1 / Fragment: SARA SBD domain, residues 773-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O95405
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.8 M1reservoirNaCl
2100 mMsodium acetate1reservoirpH5.0
320 mMTris1droppH7.4
410 mM1dropNaCl
50.1 mMEDTA1drop
61 mMdithiothreitol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 5.0.11
SYNCHROTRONSSRL BL7-12
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 20, 2000
ADSC QUANTUM 42CCDJul 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.74→43.44 Å / Num. obs: 8049 / % possible obs: 0.928 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.7 Å2
Reflection shellResolution: 2.74→2.8 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.12 / Num. unique all: 567 / % possible all: 0.998
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 7498 / % possible obs: 0.93 % / Num. measured all: 48600 / Rmerge(I) obs: 0.139
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.87 Å / % possible obs: 99.8 % / Num. unique obs: 556 / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→43.44 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 401 5.4 %RANDOM
Rwork0.227 ---
obs0.227 7401 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.8242 Å2 / ksol: 0.369255 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.69 Å20 Å20 Å2
2---16.82 Å20 Å2
3---27.5 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.74→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 16 0 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.361.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it3.822
X-RAY DIFFRACTIONc_scangle_it5.652.5
LS refinement shellResolution: 2.74→2.91 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 58 5 %
Rwork0.327 1095 -
obs--82 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3ACETATE.PAR
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 10 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / Rfactor Rwork: 0.327

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