[English] 日本語
Yorodumi
- PDB-1u7f: Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u7f
TitleCrystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
Components
  • Mothers against decapentaplegic homolog 3
  • Mothers against decapentaplegic homolog 4
KeywordsSIGNALING PROTEIN / Smad / TGF-beta / signal transduction / protein complex / phosphorylation
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / positive regulation of transforming growth factor beta3 production / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of cell proliferation involved in heart valve morphogenesis / positive regulation of transforming growth factor beta3 production / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / paraxial mesoderm morphogenesis / transdifferentiation / sterol response element binding / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / positive regulation of luteinizing hormone secretion / immune system development / filamin binding / regulation of striated muscle tissue development / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / co-SMAD 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 / neuron fate specification / bHLH transcription factor binding / response to transforming growth factor beta / positive regulation of chondrocyte differentiation / FOXO-mediated transcription of cell cycle genes / DEAD/H-box RNA helicase binding / regulation of transforming growth factor beta receptor signaling pathway / pericardium development / secondary palate development / negative regulation of osteoblast proliferation / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / brainstem development / left ventricular cardiac muscle tissue morphogenesis / nuclear glucocorticoid receptor binding / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / embryonic foregut morphogenesis / negative regulation of wound healing / cardiac conduction system development / negative regulation of cardiac muscle hypertrophy / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / sulfate binding / Germ layer formation at gastrulation / primary miRNA processing / cellular response to BMP stimulus / Formation of definitive endoderm / SMAD protein signal transduction / Signaling by BMP / embryonic pattern specification / endoderm development / Signaling by Activin / outflow tract septum morphogenesis / activin receptor signaling pathway / Formation of axial mesoderm / cell-cell junction organization / Signaling by NODAL / regulation of epithelial cell proliferation / embryonic cranial skeleton morphogenesis / gastrulation with mouth forming second / I-SMAD binding / Interleukin-37 signaling / TGFBR3 expression / cardiac muscle hypertrophy in response to stress / response to angiotensin / nuclear inner membrane / signal transduction involved in regulation of gene expression / Cardiogenesis / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of ossification / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / ureteric bud development / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cytosolic calcium ion concentration / DNA-binding transcription repressor activity / adrenal gland development / branching involved in ureteric bud morphogenesis
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 3 / Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 3, 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
Revision 1.4Nov 20, 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: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 3


Theoretical massNumber of molelcules
Total (without water)70,9953
Polymers70,9953
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-26 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.471, 60.545, 205.779
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 3 / SMAD 3 / Mothers against DPP homolog 3 / Mad3 / hMAD-3 / JV15-2 / hSMAD3


Mass: 22467.271 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: SMAD3, MADH3 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P84022
#2: Protein Mothers against decapentaplegic homolog 4 / SMAD 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / hSMAD4


Mass: 26060.693 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMar 8, 2003mirrors
RIGAKU RAXIS IV2IMAGE PLATEAug 7, 2002mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni filter/Osmic mirrorMADMx-ray1
2Ni filter/Osmic mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 2.5→100 Å / Num. all: 21793 / Num. obs: 20128 / % possible obs: 92.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.5
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 3 / Num. unique all: 1110 / % possible all: 87.2

-
Processing

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

1khx


Resolution: 2.6→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
Rfree0.247 967 -random
Rwork0.232 ---
all-20128 --
obs-19161 92.4 %-
Displacement parametersBiso mean: 64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 0 255 4983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_bond_d0.008
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.246 181 -
Rwork0.232 --
obs-1110 96.5 %

+
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