[English] 日本語
Yorodumi
- PDB-1ygs: CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ygs
TitleCRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN
ComponentsSMAD4
KeywordsTUMOUR SUPPRESSOR / SMAD4 / TUMOR SUPPRESSOR C-TERMINAL DOMAIN / TGF-BETA SIGNAL MEDIATOR / BETA-SANDWICH SCAFFOLD WITH A THREE-HELIX BUNDLE
Function / homology
Function and homology information


positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / activin responsive factor complex / atrioventricular valve formation / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / activin responsive factor complex / atrioventricular valve formation / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / neuron fate specification / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / positive regulation of extracellular matrix assembly / negative regulation of cardiac muscle hypertrophy / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / sulfate binding / Germ layer formation at gastrulation / seminiferous tubule development / cellular response to BMP stimulus / Formation of definitive endoderm / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / outflow tract septum morphogenesis / gastrulation with mouth forming second / I-SMAD binding / cardiac muscle hypertrophy in response to stress / TGFBR3 expression / Cardiogenesis / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / embryonic digit morphogenesis / adrenal gland development / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / uterus development / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / developmental growth / epithelial to mesenchymal transition / anatomical structure morphogenesis / BMP signaling pathway / single fertilization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of cardiac muscle cell apoptotic process / ovarian follicle development / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / axon guidance / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / transcription corepressor binding / cellular response to glucose stimulus / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / positive regulation of miRNA transcription / transcription coactivator binding / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / intracellular iron ion homeostasis
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsShi, Y. / Hata, A. / Lo, R.S. / Massague, J. / Pavletich, N.P.
CitationJournal: Nature / Year: 1997
Title: A structural basis for mutational inactivation of the tumour suppressor Smad4.
Authors: Shi, Y. / Hata, A. / Lo, R.S. / Massague, J. / Pavletich, N.P.
History
DepositionOct 3, 1997Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMAD4


Theoretical massNumber of molelcules
Total (without water)25,5111
Polymers25,5111
Non-polymers00
Water2,486138
1
A: SMAD4

A: SMAD4

A: SMAD4


Theoretical massNumber of molelcules
Total (without water)76,5333
Polymers76,5333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation83_555y,-z+1/2,-x+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
Unit cell
Length a, b, c (Å)197.842, 197.842, 197.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

-
Components

#1: Protein SMAD4 / DPC4 / HMAD4 / MADR4


Mass: 25511.090 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 319 - 552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 (DE3)
Cellular location: CYTOPLASM (CAN BE TRANSLOCATED INTO NUCLEUS)
Plasmid: BL21 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: 100 MM NAMES, PH6.5, 25% PEG MONOMETHYLETHER 5000, 5 MM DTT, 200 MM (NH4)2SO4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
2100 mMMES1reservoir
325 %mPEG50001reservoir
4200 mMammonium sulfate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Jul 4, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 18650 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5 / Redundancy: 5.2 % / Rsym value: 0.039 / Net I/σ(I): 32
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.162 / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 30691 / Rmerge(I) obs: 0.065

-
Processing

Software
NameClassification
DMmodel building
SQUASHphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→6 Å / Cross valid method: R FACTOR / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.279 742 5 %RANDOM
Rwork0.219 ---
obs0.219 16157 86.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 156 1678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.538
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.322 90 5 %
Rwork0.316 1677 -
obs--82 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WAT

+
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