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- PDB-5xoc: Crystal structure of human Smad3-FoxH1 complex -

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Basic information

Entry
Database: PDB / ID: 5xoc
TitleCrystal structure of human Smad3-FoxH1 complex
Components
  • Mothers against decapentaplegic homolog 3
  • Thioredoxin 1,Forkhead box protein H1
KeywordsTRANSCRIPTION / transcription factor / complex
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 / activin responsive factor complex / secondary heart field specification / embryonic heart tube anterior/posterior pattern specification ...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 / activin responsive factor complex / secondary heart field specification / embryonic heart tube anterior/posterior pattern specification / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / immune system development / regulation of striated muscle tissue development / cardiac right ventricle morphogenesis / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / co-SMAD binding / RUNX3 regulates BCL2L11 (BIM) transcription / aorta morphogenesis / bHLH transcription factor binding / determination of left/right asymmetry in lateral mesoderm / positive regulation of chondrocyte differentiation / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / pericardium development / negative regulation of osteoblast proliferation / negative regulation of intracellular estrogen receptor signaling pathway / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / 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 / signal transduction involved in regulation of gene expression / SMAD protein signal transduction / embryonic pattern specification / endoderm development / activin receptor signaling pathway / hepatocyte differentiation / ventricular trabecula myocardium morphogenesis / Signaling by Activin / Formation of axial mesoderm / cell-cell junction organization / axial mesoderm development / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / TGFBR3 expression / negative regulation of ossification / nuclear inner membrane / positive regulation of positive chemotaxis / osteoblast development / negative regulation of cardiac muscle hypertrophy in response to stress / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / ureteric bud development / DNA-binding transcription repressor activity / negative regulation of cytosolic calcium ion concentration / adrenal gland development / nuclear androgen receptor binding / negative regulation of fat cell differentiation / DNA polymerase processivity factor activity / cellular response to cytokine stimulus / SMAD binding / heart looping / R-SMAD binding / TGF-beta receptor signaling activates SMADs / outflow tract morphogenesis / thyroid gland development / mesoderm formation / protein-disulfide reductase activity / positive regulation of SMAD protein signal transduction / anatomical structure morphogenesis / developmental growth / positive regulation of focal adhesion assembly / negative regulation of osteoblast differentiation / cis-regulatory region sequence-specific DNA binding / regulation of immune response / phosphatase binding / positive regulation of bone mineralization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / somitogenesis / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to transforming growth factor beta stimulus / positive regulation of stress fiber assembly / extrinsic apoptotic signaling pathway
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. ...: / : / 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 / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / SMAD-like domain superfamily / Tumour Suppressor Smad4 / Thioredoxin / Thioredoxin / SMAD/FHA domain superfamily / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Forkhead box protein H1 / Thioredoxin 1 / Mothers against decapentaplegic homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMiyazono, K. / Ito, T. / Tanokura, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS KAKENHI15K14708 Japan
JSPS KAKENHI23228003 Japan
CitationJournal: Sci Signal / Year: 2018
Title: Hydrophobic patches on SMAD2 and SMAD3 determine selective binding to cofactors
Authors: Miyazono, K.I. / Moriwaki, S. / Ito, T. / Kurisaki, A. / Asashima, M. / Tanokura, M.
History
DepositionMay 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 3
B: Thioredoxin 1,Forkhead box protein H1


Theoretical massNumber of molelcules
Total (without water)37,9012
Polymers37,9012
Non-polymers00
Water64936
1
A: Mothers against decapentaplegic homolog 3
B: Thioredoxin 1,Forkhead box protein H1

A: Mothers against decapentaplegic homolog 3
B: Thioredoxin 1,Forkhead box protein H1

A: Mothers against decapentaplegic homolog 3
B: Thioredoxin 1,Forkhead box protein H1


Theoretical massNumber of molelcules
Total (without water)113,7036
Polymers113,7036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area11100 Å2
ΔGint-70 kcal/mol
Surface area42330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.865, 131.865, 91.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Mothers against decapentaplegic homolog 3 / hMAD-3 / JV15-2 / SMAD family member 3 / hSMAD3


Mass: 22463.471 Da / Num. of mol.: 1 / Fragment: UNP residues 220-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3, MADH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#2: Protein Thioredoxin 1,Forkhead box protein H1 / Trx-1 / Forkhead activin signal transducer 1 / hFAST-1 / Forkhead activin signal transducer 2 / Fast-2


Mass: 15437.642 Da / Num. of mol.: 1 / Fragment: UNP residues 2-109,UNP residues 322-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: trxA, fipA, tsnC, b3781, JW5856, FOXH1, FAST1, FAST2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25, UniProt: O75593
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.45 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1 M citrate pH 5.4, 0.8% ethylene imine polymer and 0.5 M NaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→114.198 Å / Num. obs: 34534 / % possible obs: 99.2 % / Redundancy: 11.7 % / Biso Wilson estimate: 43.31 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.087 / Rsym value: 0.083 / Net I/av σ(I): 8.8 / Net I/σ(I): 22.6 / Num. measured all: 218635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.20.82211340425630.3920.9150.822296.7
2.53-2.687.50.5871.31905025450.2290.6310.5873.499.2
2.68-2.8711.40.4081.92760224170.1260.4280.4086.4100
2.87-3.114.50.2862.73250022350.0780.2970.28610.8100
3.1-3.3914.50.1515.13033720920.0410.1570.15118.7100
3.39-3.7914.40.089.72743019010.0220.0830.0831.3100
3.79-4.3814.30.04914.52409016900.0130.0510.04945.9100
4.38-5.3714.10.03817.92051414590.010.040.03857.5100
5.37-7.5913.60.04615.71573511580.0130.0480.04651.1100
7.59-19.88312.20.02721.379736520.0080.0280.02776.594.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJS

1mjs


Resolution: 2.4→19.883 Å / FOM work R set: 0.7964 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 25.62 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2353 1775 5.14 %
Rwork0.1963 32759 -
obs0.1983 34534 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.86 Å2 / Biso mean: 71.23 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 2.4→19.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 0 36 2596
Biso mean---50.6 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042623
X-RAY DIFFRACTIONf_angle_d0.8163567
X-RAY DIFFRACTIONf_chiral_restr0.031394
X-RAY DIFFRACTIONf_plane_restr0.004462
X-RAY DIFFRACTIONf_dihedral_angle_d12.848945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.46490.38411380.34592367250595
2.4649-2.53730.32561410.31962477261897
2.5373-2.6190.3411330.28422490262399
2.619-2.71240.26261370.261525362673100
2.7124-2.82070.35041400.240825662706100
2.8207-2.94870.23031330.21425092642100
2.9487-3.10360.25341380.212425502688100
3.1036-3.29730.22221250.185625382663100
3.2973-3.55050.21061650.17725322697100
3.5505-3.90540.21421440.175325292673100
3.9054-4.46490.19981140.159925572671100
4.4649-5.60440.17871330.167725502683100
5.6044-19.88370.25431340.182125582692100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.517-1.75263.38421.4949-0.69564.24870.0192-0.65970.33580.0731-0.0871-0.240.2022-0.0720.31880.4686-0.00750.00380.35920.01180.5528-60.496125.86913.6918
29.2332.41450.75344.334-0.3253.69980.3647-0.68440.29890.4376-0.23730.62720.1158-0.1043-0.13460.447-0.02680.06550.35450.02410.463-74.167625.4638.1066
36.48452.97021.41585.8705-2.45297.89290.09280.61540.1436-0.25530.12610.9690.2416-0.3713-0.50110.29590.0344-0.00880.36410.0470.4926-79.425328.6262-8.5347
45.7737-5.82166.95165.895-6.68388.5482-0.0123-0.7499-0.59341.2126-0.12710.6113-0.0598-0.2305-0.09320.5022-0.01810.04350.4460.12160.6071-73.87216.7564.168
52.50371.8273-2.23953.3094-1.04453.3597-0.0182-0.1023-0.42880.2707-0.15150.00970.30070.28620.14230.37290.0015-0.02850.30790.07520.5368-65.644710.4649-1.9176
63.29330.98052.05322.60720.75874.58390.32970.316-0.25590.060.0067-0.75920.25220.8177-0.25130.40570.0374-0.0280.42680.0330.7206-52.426716.27880.2654
78.0952-4.184-4.57143.3955.22399.7187-0.06130.8082-0.661-0.8307-0.23711.0430.33480.0040.38380.55740.0046-0.08160.37420.03560.3839-69.478217.6904-14.7282
89.77662.18057.98884.59310.41666.90910.15110.0647-0.29570.4234-0.1091-0.70410.12670.29330.09890.3671-0.0041-0.05670.35290.0550.4648-52.418223.68914.153
94.17631.0041-0.5118.7725-3.91017.20480.19690.46490.6495-1.5824-0.1968-0.90750.2374-0.3243-0.03931.08530.04920.25850.74470.14340.9476-43.0776-5.4004-20.9863
104.1218-2.17770.44011.64480.99023.86230.3360.121-0.1584-0.3255-0.0889-0.7126-0.27670.72330.11570.5143-0.0467-0.00130.39510.00550.5403-56.53999.7558-10.2839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 246 )A221 - 246
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 269 )A247 - 269
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 288 )A270 - 288
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 298 )A289 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 337 )A299 - 337
6X-RAY DIFFRACTION6chain 'A' and (resid 338 through 375 )A338 - 375
7X-RAY DIFFRACTION7chain 'A' and (resid 376 through 393 )A376 - 393
8X-RAY DIFFRACTION8chain 'A' and (resid 394 through 414 )A394 - 414
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 317 )B - D213 - 317
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 345 )B - D318 - 345

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