[English] 日本語
Yorodumi
- PDB-1mhd: CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mhd
TitleCRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA
Components
  • (DNA) x 2
  • SMAD3
KeywordsCOMPLEX (TRANSCRIPTION ACTIVATOR/DNA) / COMPLEX (TRANSCRIPTION ACTIVATOR-DNA) / SMAD3 MH1 / SMAD BINDING ELEMENT / DNA / COMPLEX (TRANSCRIPTION ACTIVATOR-DNA) 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 / transdifferentiation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...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 / transdifferentiation / 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 / regulation of transforming growth factor beta2 production / heteromeric SMAD protein complex / co-SMAD binding / RUNX3 regulates BCL2L11 (BIM) transcription / 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 / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / 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 / 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 / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / heart looping / TGF-beta receptor signaling activates SMADs / positive regulation of focal adhesion assembly / R-SMAD binding / thyroid gland development / 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 / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / negative regulation of miRNA transcription / Downregulation of TGF-beta receptor signaling / T cell activation / liver development / ubiquitin binding / positive regulation of interleukin-1 beta production / nuclear receptor binding / promoter-specific chromatin binding / cellular response to glucose stimulus / positive regulation of DNA-binding transcription factor activity / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / wound healing / negative regulation of cell growth / negative regulation of protein catabolic process
Similarity search - Function
Smad3; Chain A / SMAD 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 ...Smad3; Chain A / SMAD 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsShi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling.
Authors: Shi, Y. / Wang, Y.F. / Jayaraman, L. / Yang, H. / Massague, J. / Pavletich, N.P.
History
DepositionAug 18, 1998Processing site: NDB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA
D: DNA
A: SMAD3
B: SMAD3


Theoretical massNumber of molelcules
Total (without water)39,3334
Polymers39,3334
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.600, 60.400, 71.600
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain DNA


Mass: 3959.612 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA


Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein SMAD3 / SMAD N-DOMAIN


Mass: 15539.169 Da / Num. of mol.: 2 / Fragment: MH1 DOMAIN, RESIDUES 1 - 144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SMAD / Plasmid: PGEX / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P84022
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.43 Å3/Da / Density % sol: 36 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMcitrate1reservoir
228 %PEG20001reservoir
3100 mMammonium acetate1reservoir
45 mM1reservoirMgCl2
520 mMdithiothreitol1reservoir
61 mMprotein1drop

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 9228 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.053 / Net I/σ(I): 33
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 9 / Rsym value: 0.162 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 39338 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.162

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→8 Å / Cross valid method: R FACTOR / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 402 5 %RANDOM
Rwork0.212 ---
obs0.212 8490 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 548 0 24 2614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.734
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: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.382 39 5 %
Rwork0.34 870 -
obs--81.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.34

+
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