[English] 日本語
Yorodumi
- PDB-2dq5: solution structure of the Mid1 B Box2 Chc(D/C)C2H2 Zinc-Binding D... -

+
Open data


ID or keywords:

Loading...

-
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-1Mean line
KeywordsLIGASE / E3 Ligase / RING like / Zinc coordination
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
CD2-Gal4 - #20 / Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / CD2-Gal4 / B-box, C-terminal / B-Box C-terminal domain ...CD2-Gal4 - #20 / Midline-1 / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / CD2-Gal4 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Midline-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5213
Polymers5,3901
Non-polymers1312
Water0
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

-
Components

#1: Protein/peptide Midline-1 / Mean line / 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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
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