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- PDB-2dq5: solution structure of the Mid1 B Box2 Chc(D/C)C2H2 Zinc-Binding D... -

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Basic information

Entry
Database: PDB / ID: 2dq5
Titlesolution structure of the Mid1 B Box2 Chc(D/C)C2H2 Zinc-Binding Domain: insights into an evolutionary conserved ring fold
ComponentsMidline-1
KeywordsLIGASE / E3 Ligase / RING like / Zinc coordination
Function / homology
Function and homology information


protein localization to microtubule / positive regulation of stress-activated MAPK cascade / pattern specification process / negative regulation of microtubule depolymerization / microtubule associated complex / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization / centriolar satellite ...protein localization to microtubule / positive regulation of stress-activated MAPK cascade / pattern specification process / negative regulation of microtubule depolymerization / microtubule associated complex / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization / centriolar satellite / spindle / Interferon gamma signaling / transferase activity / microtubule binding / microtubule / ubiquitin protein ligase binding / enzyme binding / Golgi apparatus / protein homodimerization activity / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
CD2-Gal4 - #20 / Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / CD2-Gal4 / : / ANCHR-like B-box zinc-binding domain ...CD2-Gal4 - #20 / Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / CD2-Gal4 / : / ANCHR-like B-box zinc-binding domain / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Fibronectin type III domain / Ring finger / 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 / Few Secondary Structures / Irregular / 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 / torsion angle dynamics, low target function
AuthorsMassiah, M.A. / Matts, J.A.B. / Short, K.M. / Simmons, B.N. / Singireddy, S. / Zou, J. / Cox, T.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure of the MID1 B-box2 CHC(D/C)C(2)H(2) Zinc-binding Domain: Insights into an Evolutionarily Conserved RING Fold
Authors: Massiah, M.A. / Matts, J.A.B. / Short, K.M. / Simmons, B.N. / Singireddy, S. / Yi, Z. / Cox, T.C.
History
DepositionMay 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)5,5213
Polymers5,3901
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure, lowest energy, fewest violations, closest to the average

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Components

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


Mass: 5390.228 Da / Num. of mol.: 1 / Fragment: Bbox2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID1 / Plasmid: pGEX-4T2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-H1 HSQC
121HNCA and HN(CA)CB
1313D-1H-15N-15N-HSQC-NOESY-HSQC
1411H-15N-NOESY-HSQC and 1H-13C-NOESY-HSQC
15115N-1H HSQC
1611H-13C-(H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.75-1.0mM 15N & 15N/13C labeled BBOX2; 50mM Tris-HCL, 100mM NaCl, 1mM ZnCl2, 10mM beta-mercaptoethanol; 2% sodium azide; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM Tris-HCl; 100mM NaCl; 5mM ZnCl2, 10mM beta-mercaptoethanol
pH: 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, F., Grzesiek, S., Vuister, G.W., Zhu, G. Pfeifer, J., Bax, A.processing
Sparky3.11Goddard, T.D., Kneller, D.G.data analysis
TALOSCornilescu, G. Delaglio, F., Bax, A.data analysis
CYANA2.1Guentert, P.refinement
RefinementMethod: torsion angle dynamics, low target function / Software ordinal: 1
Details: A total of 200 random structures were calculated with CYANA2.1 using a fast torsion angle dynamics algorithm and the best structures were selected based on their low target function (less 1) ...Details: A total of 200 random structures were calculated with CYANA2.1 using a fast torsion angle dynamics algorithm and the best structures were selected based on their low target function (less 1), no NOE violation less than 0.2 Ang, vdw < 0.25, dihedral <3o.
NMR representativeSelection criteria: minimized average structure, lowest energy, fewest violations, closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 16

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