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- PDB-5im8: Solution Structure of the Microtubule-Targeting COS Domain of MID1 -

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Basic information

Entry
Database: PDB / ID: 5im8
TitleSolution Structure of the Microtubule-Targeting COS Domain of MID1
ComponentsE3 ubiquitin-protein ligase Midline-1
KeywordsLIGASE / helix-loop-helix / microtubules / spectrin
Function / homology
Function and homology information


positive regulation of stress-activated MAPK cascade / protein localization to microtubule / pattern specification process / negative regulation of microtubule depolymerization / microtubule associated complex / centriolar satellite / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization ...positive regulation of stress-activated MAPK cascade / protein localization to microtubule / pattern specification process / negative regulation of microtubule depolymerization / microtubule associated complex / centriolar satellite / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization / spindle / Interferon gamma signaling / transferase activity / microtubule binding / microtubule / ubiquitin protein ligase binding / Golgi apparatus / enzyme binding / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger ...Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Midline-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWright, K.M. / Du, H. / Dagnachew, M. / Massiah, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1052520, MAM United States
CitationJournal: Febs J. / Year: 2016
Title: Solution structure of the microtubule-targeting COS domain of MID1.
Authors: Wright, K.M. / Du, H. / Dagnachew, M. / Massiah, M.A.
History
DepositionMar 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4Nov 3, 2021Group: Data collection / Database references / Category: database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)7,7561
Polymers7,7561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60target function
RepresentativeModel #1target function

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Components

#1: Protein E3 ubiquitin-protein ligase Midline-1 / Midin / Putative transcription factor XPRF / RING finger protein 59 / RING finger protein Midline-1 ...Midin / Putative transcription factor XPRF / RING finger protein 59 / RING finger protein Midline-1 / Tripartite motif-containing protein 18


Mass: 7755.716 Da / Num. of mol.: 1 / Fragment: COS Domain (UNP residues 320-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID1, FXY, RNF59, TRIM18, XPRF
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O15344, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HNCO
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O
Label: MID1 COS Domain / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTRISnatural abundance1
10 mMbeta-mercaptoethanolnatural abundance1
0.2 %sodium azidenatural abundance1
Sample conditionsIonic strength: 0 mM / Label: Conditions_1 / pH: 7.8 / Pressure: 1 atm / Temperature: 37 C

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 60 / Conformers submitted total number: 20

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