[English] 日本語
Yorodumi
- PDB-1u7v: Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u7v
TitleCrystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex
Components
  • Mothers against decapentaplegic homolog 2
  • Mothers against decapentaplegic homolog 4
KeywordsSIGNALING PROTEIN / Smad / TGF-beta / signal transduction / protein complex / phosphorylation
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 / zygotic specification of dorsal/ventral axis / regulation of binding / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / homomeric SMAD protein complex ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / zygotic specification of dorsal/ventral axis / regulation of binding / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / endoderm formation / positive regulation of follicle-stimulating hormone secretion / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / neuron fate specification / odontoblast differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / filamin binding / determination of left/right asymmetry in lateral mesoderm / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / response to transforming growth factor beta / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / atrioventricular canal development / embryonic foregut morphogenesis / cardiac conduction system development / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / sulfate binding / pulmonary valve morphogenesis / Signaling by BMP / signal transduction involved in regulation of gene expression / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / Formation of axial mesoderm / positive regulation of BMP signaling pathway / SMAD protein signal transduction / Signaling by NODAL / embryonic cranial skeleton morphogenesis / cardiac muscle hypertrophy in response to stress / response to cholesterol / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / aortic valve morphogenesis / pancreas development / endothelial cell activation / Cardiogenesis / insulin secretion / RUNX3 regulates CDKN1A transcription / ureteric bud development / anterior/posterior pattern specification / endocardial cushion morphogenesis / organ growth / branching involved in ureteric bud morphogenesis / adrenal gland development / embryonic digit morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling activates SMADs / SMAD binding / single fertilization / R-SMAD binding / uterus development / positive regulation of SMAD protein signal transduction / mesoderm formation / developmental growth / gastrulation
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 / Mothers against decapentaplegic homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / de Caestecker, M. / Lin, K.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural basis of heteromeric smad protein assembly in tgf-Beta signaling
Authors: Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / De Caestecker, M. / Lin, K.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 2
C: Mothers against decapentaplegic homolog 2
B: Mothers against decapentaplegic homolog 4


Theoretical massNumber of molelcules
Total (without water)70,7343
Polymers70,7343
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-27 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.240, 59.951, 207.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mothers against decapentaplegic homolog 2 / / SMAD 2 / Mothers against DPP homolog 2 / Mad-related protein 2 / hMAD-2 / JV18-1 / hSMAD2


Mass: 22499.336 Da / Num. of mol.: 2 / Fragment: MH2 and Linker domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2, MADH2, MADR2 / Plasmid: pTXB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q15796
#2: Protein Mothers against decapentaplegic homolog 4 / / SMAD 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / hSMAD4


Mass: 25735.330 Da / Num. of mol.: 1 / Fragment: MH2 and Linker domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, MADH4, DPC4 / Plasmid: pGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q13485

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2002 / Details: mirrors
RadiationMonochromator: Ni filter/Osmic mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 17632 / Num. obs: 14546 / % possible obs: 82.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1353 / % possible all: 84.4

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHX

1khx


Resolution: 2.7→100 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1485 -random
Rwork0.243 ---
all-17632 --
obs-14546 82.5 %-
Displacement parametersBiso mean: 67.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 0 0 4777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.011
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.279 --
Rwork0.243 --
obs-1353 85.3 %

+
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