[English] 日本語
Yorodumi
- PDB-9hwe: SMAD4 MH2, residues 314-552 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hwe
TitleSMAD4 MH2, residues 314-552
ComponentsMothers against decapentaplegic homolog 4
KeywordsTRANSCRIPTION / Transcription factor / SMAD4 MH2 domain
Function / homology
Function and homology information


: / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / epithelial cell migration / SMAD protein complex ...: / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / epithelial cell migration / SMAD protein complex / neuron fate specification / cardiac muscle hypertrophy in response to stress / heteromeric SMAD protein complex / RUNX2 regulates bone development / filamin binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / left ventricular cardiac muscle tissue morphogenesis / cardiac conduction system development / positive regulation of extracellular matrix assembly / atrioventricular canal development / Transcriptional regulation of pluripotent stem cells / sulfate binding / negative regulation of cardiac muscle hypertrophy / Germ layer formation at gastrulation / SMAD protein signal transduction / cellular response to BMP stimulus / Signaling by BMP / Formation of definitive endoderm / Signaling by Activin / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by NODAL / adrenal gland development / I-SMAD binding / embryonic digit morphogenesis / TGFBR3 expression / Cardiogenesis / endothelial cell activation / RUNX3 regulates CDKN1A transcription / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / ovarian follicle development / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / ERK1 and ERK2 cascade / BMP signaling pathway / epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis / positive regulation of cardiac muscle cell apoptotic process / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / transcription corepressor binding / cellular response to glucose stimulus / negative regulation of protein catabolic process / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of cell growth / positive regulation of miRNA transcription / transcription coactivator binding / osteoblast differentiation / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / intracellular signal transduction / transcription cis-regulatory region binding / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA-templated transcription
Similarity search - Function
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 ...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 / SMAD/FHA domain superfamily
Similarity search - Domain/homology
SMAD family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTorner, C. / Condeminas, M. / Pluta, R. / Pous, J. / Macias, M.J.
Funding support Spain, 5items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2017-82675-P Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-122909NB-I00 Spain
Generalitat de Catalunya2021 SGR-866 Spain
Other privateBBVA
Ministerio de Ciencia e Innovacion (MCIN)PDC_2021-121162-I00 Spain
CitationJournal: To Be Published
Title: (RUNNING TITLE:) Insights into the structure-activity relationship of SMAD4 variants linked to Myhre syndrome and hereditary hemorrhagic telangiectasia
Authors: Torner, C. / Condeminas, M. / Pluta, R. / Aragon, E. / Khan, R.J. / Martin-Malpartida, P. / Rodriguez de Regil, M. / Pous, J. / Humm, A.-S. / Niebling, S. / Garcia-Alai, M. / Marquez, J.A. / ...Authors: Torner, C. / Condeminas, M. / Pluta, R. / Aragon, E. / Khan, R.J. / Martin-Malpartida, P. / Rodriguez de Regil, M. / Pous, J. / Humm, A.-S. / Niebling, S. / Garcia-Alai, M. / Marquez, J.A. / Martinez, A. / Macias, M.J.
History
DepositionJan 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4966
Polymers26,1181
Non-polymers3785
Water2,108117
1
A: Mothers against decapentaplegic homolog 4
hetero molecules

A: Mothers against decapentaplegic homolog 4
hetero molecules

A: Mothers against decapentaplegic homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,48818
Polymers78,3533
Non-polymers1,13515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation83_555y,-z+1/2,-x+1/21
Buried area7340 Å2
ΔGint-35 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.572, 196.572, 196.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Components on special symmetry positions
IDModelComponents
11A-817-

HOH

-
Components

#1: Protein Mothers against decapentaplegic homolog 4 / MAD homolog 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD ...MAD homolog 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD family member 4 / SMAD 4 / Smad4 / hSMAD4


Mass: 26117.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, DPC4, MADH4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5 100 nL sample + 200 nL precipitant solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→113.491 Å / Num. obs: 33864 / % possible obs: 96.3 % / Redundancy: 36.8 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 1 / Net I/σ(I): 29.1
Reflection shellResolution: 1.7→1.771 Å / Redundancy: 22.1 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1693 / CC1/2: 0.313 / % possible all: 56.7

-
Processing

Software
NameVersionClassification
autoPROC1.0.5 (20240123)data processing
XDSJun 30, 2024 (BUILT 20241002)data reduction
Aimless0.7.13data scaling
PHASER1.18.2-3874-000phasing
PHENIX1.21rc1_5107refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→59.27 Å / SU ML: 0.1332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1906 1696 5.01 %
Rwork0.1779 32167 -
obs0.1785 33863 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 22 117 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071632
X-RAY DIFFRACTIONf_angle_d1.12972211
X-RAY DIFFRACTIONf_chiral_restr0.0626234
X-RAY DIFFRACTIONf_plane_restr0.0129286
X-RAY DIFFRACTIONf_dihedral_angle_d18.3464603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.3083370.289840X-RAY DIFFRACTION29.9
1.75-1.810.29491390.2832676X-RAY DIFFRACTION95.39
1.81-1.870.27231410.24122807X-RAY DIFFRACTION99.93
1.88-1.950.24761510.20912795X-RAY DIFFRACTION100
1.95-2.040.22051480.17112810X-RAY DIFFRACTION100
2.04-2.150.20381710.17282783X-RAY DIFFRACTION100
2.15-2.280.18071700.16012811X-RAY DIFFRACTION100
2.28-2.460.1731490.16722856X-RAY DIFFRACTION100
2.46-2.70.20141440.18442849X-RAY DIFFRACTION100
2.7-3.090.16021730.17932867X-RAY DIFFRACTION100
3.1-3.890.1761410.15382919X-RAY DIFFRACTION100
3.9-59.270.19191320.18073154X-RAY DIFFRACTION100
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)
11.956581012230.6244616981691.288825765336.29091495653-2.028287802414.811965179610.150833476872-0.0761263249941-0.051265671099-0.178023810653-0.06966713573840.510159397292-0.0716475229516-0.552026346582-0.1978765313070.3943020293740.107514208642-0.180359515710.516585001725-0.1034219850790.3309483655158.6914687902531.586361326745.4892291799
22.42500676891-1.742531363870.4995728948375.16604917742-1.517298754363.664840207590.101726865068-0.0158814292816-0.568019248453-0.07508107255510.1529743151010.8020113487990.507769392551-0.752090087302-0.1816513464840.310785883518-0.047224378528-0.1143148956470.427137739853-0.09944444801950.39444579000816.473704755816.433272418958.453470606
33.02255640088-2.042646612691.653469477888.33879970876-2.991477210094.6927298292-0.05034705462750.2503146257940.282141912689-0.442035872556-0.06710405745570.378804705466-0.451234294956-0.2542128116160.0450412962240.3226183707290.10798630721-0.1584777969960.335222814885-0.115923074760.27151665461516.774738441333.415309161552.7941948201
42.547634909010.2317824975850.0230599858262.55084575001-0.7374542659444.469318546990.05536762096940.140059430299-0.136341141611-0.0281611285307-0.0202818941421-0.14017968990.1415846392950.239754692804-0.01784885437850.2149604324960.0876251523663-0.09985352151270.234599099278-0.1346706302560.24508862317231.996825971520.043398054459.3450143315
52.82983722225-0.5998680976330.182230722653.25584380326-0.469077923832.947777102660.03966153518540.234844307879-0.204661443583-0.2568964166210.07706836614050.103960722520.370113475828-0.260379788872-0.174827850790.3619353041790.0366212973728-0.1401918489420.42713851343-0.1291458533140.27227792604220.659993179915.508858664546.8595294822
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 440 through 456 )440 - 456123 - 139
22chain 'A' and (resid 457 through 523 )457 - 523140 - 174
33chain 'A' and (resid 524 through 545 )524 - 545175 - 196
44chain 'A' and (resid 318 through 392 )318 - 3921 - 75
55chain 'A' and (resid 393 through 439 )393 - 43976 - 122

+
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