[English] 日本語
Yorodumi
- PDB-8f37: AbdA Homeodomain NMR Solution Structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f37
TitleAbdA Homeodomain NMR Solution Structure
ComponentsHomeobox protein abdominal-A
KeywordsDNA BINDING PROTEIN / Homeodomain AbdA / Transcription factor
Function / homology
Function and homology information


: / oenocyte differentiation / dorsal vessel heart proper cell fate commitment / positive regulation of muscle organ development / determination of genital disc primordium / gonadal mesoderm development / oenocyte development / mesodermal cell fate specification / cardioblast differentiation / genital disc anterior/posterior pattern formation ...: / oenocyte differentiation / dorsal vessel heart proper cell fate commitment / positive regulation of muscle organ development / determination of genital disc primordium / gonadal mesoderm development / oenocyte development / mesodermal cell fate specification / cardioblast differentiation / genital disc anterior/posterior pattern formation / neuroblast development / muscle cell fate specification / neuroblast fate determination / polytene chromosome band / gonad development / genitalia development / peripheral nervous system development / germ cell migration / cardiac muscle tissue development / anterior/posterior pattern specification / midgut development / cis-regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / heart development / nervous system development / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox protein / Homeobox protein / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeobox protein abdominal-A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsBeasley, S.A. / Simons, R.A. / Advocate, M.R. / Mekkaoui, F. / Spratt, D.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R5GM126432 United States
CitationJournal: To Be Published
Title: AbdA Homeodomain NMR solution structure
Authors: Beasley, S.A. / Simons, R.A. / Advocate, M.R. / Mekkaoui, F. / Spratt, D.E.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox protein abdominal-A


Theoretical massNumber of molelcules
Total (without water)7,9231
Polymers7,9231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer at expected MW
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Homeobox protein abdominal-A


Mass: 7923.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: abd-A, CG10325 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29555

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HNCO
191isotropic13D HN(CO)CA
181isotropic13D (H)CCH-TOCSY aromatic
171isotropic13D (H)CCH-TOCSY aliphatic
161isotropic13D HN(CA)CO
1101isotropic13D C(CO)NH
1121isotropic13D CBCA(CO)NH
1111isotropic13D HN(CA)CB
1141isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-13C NOESY aliphatic
1161isotropic13D H(CCO)NH

-
Sample preparation

DetailsType: solution
Contents: 0.857 mM [U-100% 13C; U-100% 15N] AbdAHD, 20 mM MES, 100 mM NaCl, 2 mM TCEP, 5 mM MgCl2, 90% H2O/10% D2O
Label: AbdAHD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.857 mMAbdAHD[U-100% 13C; U-100% 15N]1
20 mMMESnatural abundance1
100 mMNaClnatural abundance1
2 mMTCEPnatural abundance1
5 mMMgCl2natural abundance1
Sample conditionsIonic strength: 128 mM / Label: standard / pH: 6.0 Not defined / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Agilent INOVA AVANCE / Manufacturer: Agilent / Model: INOVA AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntertrefinement
NMRViewJ9.1.0-b63One Moon Scientificchemical shift assignment
NMRViewJ9.1.0-b63One Moon Scientificpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntertstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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