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- PDB-2jun: Structure of the MID1 tandem B-boxes reveals an interaction remin... -

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Basic information

Entry
Database: PDB / ID: 2jun
TitleStructure of the MID1 tandem B-boxes reveals an interaction reminiscent of intermolecular RING heterodimers
ComponentsMidline-1Mean line
KeywordsLIGASE / MIDLINE 1 / B-box / TRIM / Ring Finger / Alternative splicing / Coiled coil / Cytoplasm / Cytoskeleton / Disease mutation / Metal-binding / Microtubule / Phosphorylation / Ubl conjugation pathway / Zinc / Zinc-finger
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. / Classic Zinc Finger / 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. / Double Stranded RNA Binding Domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Midline-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsSolution Structure of native tandem B-box domains from Midline-1 determined by NMR spectroscopy
AuthorsTao, H. / Singireddy, S. / Jakkidi, M. / Simmons, B.N. / Short, K.M. / Cox, T.C. / Massiah, M.A.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of the MID1 Tandem B-Boxes Reveals an Interaction Reminiscent of Intermolecular Ring Heterodimers
Authors: Tao, H. / Simmons, B.N. / Singireddy, S. / Jakkidi, M. / Short, K.M. / Cox, T.C. / Massiah, M.A.
History
DepositionAug 31, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Midline-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6795
Polymers11,4171
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11417.117 Da / Num. of mol.: 1 / Fragment: B-boxes type 1 and 2, residues 114-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID1, FXY, RNF59, TRIM18, XPRF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O15344, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution Structure of native tandem B-box domains from Midline-1 determined by NMR spectroscopy
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.75-1.0 mM 15N & 15N/13C labeled protein in 50 mM Tris-HCl, 300 mM NaCl, 10 mM 2-mercaptoethanol, 5 mM ZnCl2, 2 % azide, and 0.015% Triton-X 100, pH 7.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMTRIS1
300 mMsodium chloride1
10 mMbeta-mercaptoethanol1
5 mMzinc chloride1
2 %sodium azide1
0.015 %triton-X1001
10 %D2O1
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 294 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 0.84 Å / Distance rms dev error: 0.5 Å

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