[English] 日本語
Yorodumi
- PDB-5xoc: Crystal structure of human Smad3-FoxH1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / sterol response element binding / activin responsive factor complex / transdifferentiation / 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 / sterol response element binding / activin responsive factor complex / transdifferentiation / 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 / regulation of striated muscle tissue development / SMAD protein complex / immune system development / cardiac right ventricle morphogenesis / regulation of transforming growth factor beta2 production / heteromeric SMAD protein complex / co-SMAD binding / aorta morphogenesis / RUNX3 regulates BCL2L11 (BIM) transcription / determination of left/right asymmetry in lateral mesoderm / bHLH transcription factor binding / DEAD/H-box RNA helicase binding / pericardium development / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / negative regulation of androgen receptor signaling pathway / embryonic foregut morphogenesis / negative regulation of wound healing / nuclear glucocorticoid receptor binding / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / endoderm development / Formation of definitive endoderm / activin receptor signaling pathway / embryonic pattern specification / SMAD protein signal transduction / signal transduction involved in regulation of gene expression / hepatocyte differentiation / ventricular trabecula myocardium morphogenesis / axial mesoderm development / Signaling by Activin / Formation of axial mesoderm / cell-cell junction organization / embryonic cranial skeleton morphogenesis / Signaling by NODAL / regulation of epithelial cell proliferation / I-SMAD binding / Interleukin-37 signaling / response to angiotensin / TGFBR3 expression / positive regulation of positive chemotaxis / osteoblast development / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / negative regulation of cardiac muscle hypertrophy in response to stress / NOTCH4 Intracellular Domain Regulates Transcription / ureteric bud development / DNA-binding transcription repressor activity / adrenal gland development / nuclear androgen receptor binding / DNA polymerase processivity factor activity / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / heart looping / cellular response to cytokine stimulus / SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of focal adhesion assembly / outflow tract morphogenesis / R-SMAD binding / thyroid gland development / protein-disulfide reductase activity / mesoderm formation / regulation of immune response / developmental growth / anatomical structure morphogenesis / negative regulation of osteoblast differentiation / phosphatase binding / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of bone mineralization / somitogenesis / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / JNK cascade / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / extrinsic apoptotic signaling pathway / collagen 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. ...: / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more