[English] 日本語
Yorodumi
- PDB-2lb1: Structure of the second domain of human Smurf1 in complex with a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lb1
TitleStructure of the second domain of human Smurf1 in complex with a human Smad1 derived peptide
Components
  • E3 ubiquitin-protein ligase SMURF1
  • Mothers against decapentaplegic homolog 1
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / SMURF / SMAD / CDK / signal transduction / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


mesodermal cell fate commitment / substrate localization to autophagosome / engulfment of target by autophagosome / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / heteromeric SMAD protein complex / co-SMAD binding / protein targeting to vacuole involved in autophagy ...mesodermal cell fate commitment / substrate localization to autophagosome / engulfment of target by autophagosome / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / heteromeric SMAD protein complex / co-SMAD binding / protein targeting to vacuole involved in autophagy / negative regulation of muscle cell differentiation / positive regulation of cartilage development / DEAD/H-box RNA helicase binding / primary miRNA binding / gamete generation / activin receptor binding / hindbrain development / ectoderm development / cardiac conduction system development / positive regulation of dendrite extension / primary miRNA processing / transforming growth factor beta receptor binding / receptor catabolic process / SMAD protein signal transduction / Signaling by BMP / embryonic pattern specification / negative regulation of activin receptor signaling pathway / HECT-type E3 ubiquitin transferase / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / cartilage development / nuclear inner membrane / Cardiogenesis / positive regulation of dendrite development / Wnt signaling pathway, planar cell polarity pathway / ureteric bud development / SMAD binding / positive regulation of sprouting angiogenesis / midbrain development / R-SMAD binding / anatomical structure morphogenesis / negative regulation of BMP signaling pathway / cardiac muscle cell proliferation / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of axon extension / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transforming growth factor beta receptor signaling pathway / ossification / protein export from nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / protein localization to plasma membrane / Asymmetric localization of PCP proteins / male germ cell nucleus / stem cell differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / bone development / phospholipid binding / positive regulation of miRNA transcription / protein polyubiquitination / Regulation of RUNX2 expression and activity / ubiquitin-protein transferase activity / osteoblast differentiation / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / MAPK cascade / DNA-binding transcription activator activity, RNA polymerase II-specific / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / axon / negative regulation of cell population proliferation / neuronal cell body / DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 / E3 ubiquitin-protein ligase, SMURF1 type / SMAD-like domain superfamily / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / SMAD/FHA domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / C2 domain / WW/rsp5/WWP domain signature. / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 1 / E3 ubiquitin-protein ligase SMURF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMacias, M.J. / Aragon, E. / Goerner, N. / Zaromytidou, A. / Xi, Q. / Escobedo, A. / Massague, J.
CitationJournal: Genes Dev. / Year: 2011
Title: A Smad action turnover switch operated by WW domain readers of a phosphoserine code.
Authors: Aragon, E. / Goerner, N. / Zaromytidou, A.I. / Xi, Q. / Escobedo, A. / Massague, J. / Macias, M.J.
History
DepositionMar 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SMURF1
B: Mothers against decapentaplegic homolog 1


Theoretical massNumber of molelcules
Total (without water)5,6482
Polymers5,6482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide E3 ubiquitin-protein ligase SMURF1 / hSMURF1 / SMAD ubiquitination regulatory factor 1 / SMAD-specific E3 ubiquitin-protein ligase 1


Mass: 4170.647 Da / Num. of mol.: 1 / Fragment: residues 305-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMURF1, KIAA1625 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HCE7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Mothers against decapentaplegic homolog 1 / MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member ...MAD homolog 1 / Mothers against DPP homolog 1 / JV4-1 / Mad-related protein 1 / SMAD family member 1 / SMAD 1 / Smad1 / hSMAD1 / Transforming growth factor-beta-signaling protein 1 / BSP-1


Mass: 1477.592 Da / Num. of mol.: 1 / Fragment: residues 221-233 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15797
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the first domain of human Smurf1 in complex with a human Smad1 derived peptide.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1333D CBCA(CO)NH
1433D HN(CA)CB
1522D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNEDD4LWW3-11
3 mMSMAD3-21
20 mMsodium phosphate-31
100 mMsodium chloride-41
2 mMsodium azide-51
1 mMNEDD4LWW3-6[U-100% 15N]2
3 mMSMAD3-72
20 mMsodium phosphate-82
100 mMsodium chloride-92
2 mMsodium azide-102
1 mMNEDD4LWW3-11[U-100% 13C; U-100% 15N]3
3 mMSMAD3-123
20 mMsodium phosphate-133
100 mMsodium chloride-143
2 mMsodium azide-153
Sample conditionsIonic strength: 0.42 / pH: 7 / Pressure: ambient / Temperature: 285 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 711 / NOE intraresidue total count: 0 / NOE long range total count: 308 / NOE medium range total count: 51 / NOE sequential total count: 171 / Hydrogen bond constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 20

+
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