[English] 日本語
Yorodumi
- PDB-1g88: S4AFL3ARG515 MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g88
TitleS4AFL3ARG515 MUTANT
ComponentsSMAD4
KeywordsTRANSCRIPTION / transcriptional factor / L3 loop mutant
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 / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / positive regulation of luteinizing hormone secretion / filamin binding / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / 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 / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / negative regulation of cardiac muscle hypertrophy / positive regulation of extracellular matrix assembly / sulfate binding / Germ layer formation at gastrulation / cellular response to BMP stimulus / Formation of definitive endoderm / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / outflow tract septum morphogenesis / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / I-SMAD binding / TGFBR3 expression / cardiac muscle hypertrophy in response to stress / Cardiogenesis / RUNX3 regulates CDKN1A transcription / endothelial cell activation / neural crest cell differentiation / adrenal gland development / branching involved in ureteric bud morphogenesis / embryonic digit morphogenesis / interleukin-6-mediated signaling pathway / ventricular septum morphogenesis / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / uterus development / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / single fertilization / anatomical structure morphogenesis / epithelial to mesenchymal transition / developmental growth / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / ovarian follicle development / positive regulation of cardiac muscle cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to transforming growth factor beta stimulus / collagen binding / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / axon guidance / transcription corepressor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / cellular response to glucose stimulus / transcription coactivator binding / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / positive regulation of miRNA transcription / osteoblast differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / transcription by RNA polymerase II
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChako, B.M. / Qin, B. / Lam, S.S. / Correia, J.J. / Lin, K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The L3 loop and C-terminal phosphorylation jointly define Smad protein trimerization.
Authors: Chacko, B.M. / Qin, B. / Correia, J.J. / Lam, S.S. / de Caestecker, M.P. / Lin, K.
History
DepositionNov 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMAD4
B: SMAD4
C: SMAD4


Theoretical massNumber of molelcules
Total (without water)88,0453
Polymers88,0453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-18 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.855, 140.855, 194.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein SMAD4 / DPC4


Mass: 29348.332 Da / Num. of mol.: 3 / Fragment: SMAD4 ACTIVE FRAGMENT / Mutation: R515S / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13485

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES12
2250 mMlithium sulfate12
310 %(v/v)PEG400012

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 72845 / Num. obs: 19552 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5.5 / Redundancy: 3.72 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.5 / % possible all: 88
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. measured all: 72845
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 88 % / Mean I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40.5 Å / Data cutoff high absF: 191639.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 897 -RANDOM
Rwork0.203 ---
all0.19 19954 --
obs0.203 18416 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 0 0 5431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 3→3.19 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.276 2557 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rwork: 0.276

+
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