[English] 日本語
Yorodumi
- PDB-3dit: Crystal structure of MAD MH2 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dit
TitleCrystal structure of MAD MH2 domain
ComponentsProtein mothers against dpp
KeywordsSIGNALING PROTEIN / MAD / TGF-beta / MH2 / Cytoplasm / Developmental protein / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation
Function / homology
Function and homology information


Signaling by BMP / RUNX2 regulates bone development / imaginal disc morphogenesis / R8 cell fate specification / histoblast morphogenesis / negative regulation of salivary gland boundary specification / imaginal disc-derived wing vein morphogenesis / trunk segmentation / imaginal disc-derived leg morphogenesis / germ-line stem cell division ...Signaling by BMP / RUNX2 regulates bone development / imaginal disc morphogenesis / R8 cell fate specification / histoblast morphogenesis / negative regulation of salivary gland boundary specification / imaginal disc-derived wing vein morphogenesis / trunk segmentation / imaginal disc-derived leg morphogenesis / germ-line stem cell division / compound eye morphogenesis / positive regulation of neuromuscular junction development / follicle cell of egg chamber development / wing disc anterior/posterior pattern formation / positive regulation of synaptic assembly at neuromuscular junction / Ub-specific processing proteases / RNA polymerase II transcription repressor complex / intestinal stem cell homeostasis / ventral cord development / co-SMAD binding / heteromeric SMAD protein complex / imaginal disc-derived wing morphogenesis / germ-line stem cell population maintenance / SMAD protein signal transduction / I-SMAD binding / negative regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / somatic stem cell population maintenance / anatomical structure morphogenesis / BMP signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytosol / cytoplasm
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
Protein mothers against dpp
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsHao, R. / Wu, J.W. / Wang, Z.X.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Drosophila Mad MH2 domain.
Authors: Hao, R. / Chen, L. / Wu, J.W. / Wang, Z.X.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein mothers against dpp
B: Protein mothers against dpp
C: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)63,9363
Polymers63,9363
Non-polymers00
Water1,62190
1
A: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)21,3121
Polymers21,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)21,3121
Polymers21,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein mothers against dpp


Theoretical massNumber of molelcules
Total (without water)21,3121
Polymers21,3121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.864, 95.864, 66.726
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Protein mothers against dpp


Mass: 21312.010 Da / Num. of mol.: 3 / Fragment: MAD MH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mad, CG12399 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P42003
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, 0.35M Na Formate, 2% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 10156 / Num. obs: 10156 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.116
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4.01 / Num. unique all: 1126 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHU

1khu


Resolution: 3.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31 509 4.5 %random
Rwork0.244 ---
obs-9604 85 %-
Solvent computationBsol: 29.977 Å2
Displacement parametersBiso mean: 63.521 Å2
Baniso -1Baniso -2Baniso -3
1-5.801 Å2-6.9 Å20 Å2
2--5.801 Å20 Å2
3----11.602 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 0 90 4548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

+
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