[English] 日本語
Yorodumi
- PDB-1mk2: SMAD3 SBD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mk2
TitleSMAD3 SBD complex
Components
  • Madh-interacting protein
  • SMAD 3
KeywordsTRANSCRIPTION / SMAD3 / SBD / SARA
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 / sterol response element binding / transdifferentiation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / transdifferentiation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / SMAD protein complex / 1-phosphatidylinositol binding / negative regulation of osteoblast proliferation / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / bHLH transcription factor binding / trophoblast cell migration / negative regulation of transforming growth factor beta production / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / positive regulation of extracellular matrix assembly / negative regulation of wound healing / nuclear glucocorticoid receptor binding / Germ layer formation at gastrulation / primary miRNA processing / cell-cell junction organization / SMAD protein signal transduction / negative regulation of lipopolysaccharide-mediated signaling pathway / transforming growth factor beta receptor binding / Formation of definitive endoderm / signal transduction involved in regulation of gene expression / response to angiotensin / Signaling by Activin / activin receptor signaling pathway / negative regulation of ossification / Formation of axial mesoderm / ureteric bud development / regulation of dendritic spine morphogenesis / Signaling by NODAL / response to alcohol / Interleukin-37 signaling / adrenal gland development / I-SMAD binding / TGFBR3 expression / positive regulation of positive chemotaxis / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / negative regulation of fat cell differentiation / DNA-binding transcription repressor activity / endosomal transport / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of bone mineralization / negative regulation of cytosolic calcium ion concentration / R-SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / positive regulation of focal adhesion assembly / cellular response to platelet-derived growth factor stimulus / cellular response to transforming growth factor beta stimulus / regulation of immune response / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / JNK cascade / anatomical structure morphogenesis / positive regulation of stress fiber assembly / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / phosphatase binding / cis-regulatory region sequence-specific DNA binding / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / response to gamma radiation / negative regulation of miRNA transcription / apoptotic signaling pathway / regulation of mitochondrial membrane potential / nuclear receptor binding / transcription corepressor binding / wound healing / positive regulation of interleukin-1 beta production / T cell activation / Downregulation of TGF-beta receptor signaling / cellular response to glucose stimulus / response to cocaine / cellular response to virus / ubiquitin binding / negative regulation of protein catabolic process / positive regulation of protein import into nucleus / promoter-specific chromatin binding / negative regulation of inflammatory response / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of cell growth / protein-DNA complex
Similarity search - Function
Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / Tumour Suppressor Smad4 - #10 / FYVE zinc finger ...Smad anchor for receptor activation, Smad-binding domain / Smad anchor for receptor activation, Smad-binding domain superfamily / Smad anchor for receptor activation (SARA) / Smad anchor for receptor activation (SARA) / Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / Tumour Suppressor Smad4 - #10 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / 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 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Zinc finger FYVE domain-containing protein 9 / SMAD family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsQin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
CitationJournal: Genes Dev. / Year: 2002
Title: Smad3 allostery links TGF-beta receptor kinase activation to transcriptional control
Authors: Qin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMAD 3
B: Madh-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2866
Polymers27,0462
Non-polymers2404
Water00
1
A: SMAD 3
B: Madh-interacting protein
hetero molecules

A: SMAD 3
B: Madh-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,57212
Polymers54,0914
Non-polymers4808
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area10940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.995, 71.716, 86.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis:

-
Components

#1: Protein SMAD 3 / Mad3 / hMAD-3 / mMad3 / JV15-2 / hSMAD3


Mass: 23227.361 Da / Num. of mol.: 1 / Fragment: MH2 domain, residues 220-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#2: Protein/peptide Madh-interacting protein / Smad anchor for receptor activation / Receptor activation anchor / hSARA / Novel serine protease / NSP


Mass: 3818.246 Da / Num. of mol.: 1 / Fragment: SARA SBD domain, residues 773-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O95405
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails (eV)
11.8 M1reservoirNaCl
2100 mMsodium acetate1reservoirpH5.0
320 mMTris1droppH7.4
410 mM1dropNaCl
50.1 mMEDTA1drop
61 mMdithiothreitol1drop

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 5.0.11
SYNCHROTRONSSRL BL7-12
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 20, 2000
ADSC QUANTUM 42CCDJul 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.74→43.44 Å / Num. obs: 8049 / % possible obs: 0.928 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.7 Å2
Reflection shellResolution: 2.74→2.8 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.12 / Num. unique all: 567 / % possible all: 0.998
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 7498 / % possible obs: 0.93 % / Num. measured all: 48600 / Rmerge(I) obs: 0.139
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.87 Å / % possible obs: 99.8 % / Num. unique obs: 556 / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.6

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→43.44 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 401 5.4 %RANDOM
Rwork0.227 ---
obs0.227 7401 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.8242 Å2 / ksol: 0.369255 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.69 Å20 Å20 Å2
2---16.82 Å20 Å2
3---27.5 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.74→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 16 0 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.361.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it3.822
X-RAY DIFFRACTIONc_scangle_it5.652.5
LS refinement shellResolution: 2.74→2.91 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 58 5 %
Rwork0.327 1095 -
obs--82 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3ACETATE.PAR
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 10 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / Rfactor Rwork: 0.327

+
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