[English] 日本語
Yorodumi
- PDB-6irr: Solution structure of DISC1/ATF4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6irr
TitleSolution structure of DISC1/ATF4 complex
ComponentsDisrupted in schizophrenia 1 homolog,Cyclic AMP-dependent transcription factor ATF-4
KeywordsSTRUCTURAL PROTEIN / Scaffold protein / Psychiatric disorder / coiled coil
Function / homology
Function and homology information


L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / pyramidal neuron migration to cerebral cortex / ATF4-CREB1 transcription factor complex / cerebral cortex radially oriented cell migration / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / leucine zipper domain binding ...L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / pyramidal neuron migration to cerebral cortex / ATF4-CREB1 transcription factor complex / cerebral cortex radially oriented cell migration / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / leucine zipper domain binding / integrated stress response signaling / cAMP response element binding protein binding / HRI-mediated signaling / mitochondrial calcium ion homeostasis / response to manganese-induced endoplasmic reticulum stress / central region of growth cone / cell proliferation in forebrain / PERK-mediated unfolded protein response / regulation of dendritic spine development / lens fiber cell morphogenesis / cellular response to leucine starvation / regulation of synapse maturation / non-motile cilium assembly / intermediate filament cytoskeleton / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / dynein complex / positive regulation of ubiquitin-dependent protein catabolic process / kinesin complex / protein localization to centrosome / regulation of postsynapse organization / negative regulation of cold-induced thermogenesis / embryonic hemopoiesis / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cell-matrix adhesion / gamma-aminobutyric acid signaling pathway / regulation of osteoblast differentiation / positive regulation of neuroblast proliferation / regulation of neuron projection development / ciliary base / bone mineralization / positive regulation of transcription by RNA polymerase I / negative regulation of potassium ion transport / detection of temperature stimulus involved in sensory perception of pain / TOR signaling / kinesin binding / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of vascular endothelial growth factor production / positive regulation of Wnt signaling pathway / canonical Wnt signaling pathway / positive regulation of axon extension / response to electrical stimulus / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / regulation of synaptic transmission, glutamatergic / dendrite membrane / cellular response to amino acid starvation / nuclear periphery / response to endoplasmic reticulum stress / gluconeogenesis / GABA-ergic synapse / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / positive regulation of neuron projection development / microtubule cytoskeleton organization / RNA polymerase II transcription regulator complex / neuron cellular homeostasis / response to toxic substance / intracellular calcium ion homeostasis / circadian rhythm / neuron differentiation / neuron migration / positive regulation of neuron apoptotic process / intracellular protein localization / synaptic vesicle / cell body / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / molecular adaptor activity / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / transcription by RNA polymerase II / postsynaptic density / nuclear speck / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / centrosome / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding
Similarity search - Function
Disrupted in schizophrenia 1 / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
Cyclic AMP-dependent transcription factor ATF-4 / Disrupted in schizophrenia 1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsYe, F. / Yu, C. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
16104518 Hong Kong
CitationJournal: Mol. Psychiatry / Year: 2019
Title: Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders.
Authors: Wang, X. / Ye, F. / Wen, Z. / Guo, Z. / Yu, C. / Huang, W.K. / Rojas Ringeling, F. / Su, Y. / Zheng, W. / Zhou, G. / Christian, K.M. / Song, H. / Zhang, M. / Ming, G.L.
History
DepositionNov 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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: Disrupted in schizophrenia 1 homolog,Cyclic AMP-dependent transcription factor ATF-4


Theoretical massNumber of molelcules
Total (without water)14,5651
Polymers14,5651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 43structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Disrupted in schizophrenia 1 homolog,Cyclic AMP-dependent transcription factor ATF-4 / cAMP-dependent transcription factor ATF-4 / Activating transcription factor 4 / C/EBP-related ATF / ...cAMP-dependent transcription factor ATF-4 / Activating transcription factor 4 / C/EBP-related ATF / C/ATF / Tax-responsive enhancer element-binding protein 67 homolog / TaxREB67 homolog


Mass: 14565.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Disc1, Atf4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q811T9, UniProt: Q06507
Sequence detailsSequence of the protein was based on Isoform 2 of database UNP Q811T9 (DISC1_MOUSE).

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-15N NOESY
121isotropic23D 1H-13C NOESY
133isotropic12D 1H-1H NOESY
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-100% 13C; U-100% 15N] DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 100% D2O15N, 13C100% D2O
solution20.8 mM [U-99% 15N] DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 90% H2O/10% D2O15N90% H2O/10% D2O
solution30.8 mM DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 100% D2Ounlabeled100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDISC1/ATF4 complex[U-100% 13C; U-100% 15N]1
1 mMDTTnatural abundance1
1 mMEDTAnatural abundance1
100 mMpotassium phosphatenatural abundance1
0.8 mMDISC1/ATF4 complex[U-99% 15N]2
1 mMDTTnatural abundance2
1 mMEDTAnatural abundance2
100 mMpotassium phosphatenatural abundance2
0.8 mMDISC1/ATF4 complexnatural abundance3
1 mMDTTnatural abundance3
1 mMEDTAnatural abundance3
100 mMpotassium phosphatenatural abundance3
Sample conditionsIonic strength: 100mM potassium phosphate Not defined / Label: conditions1 / pH: 6.5 / Pressure: ambient Pa / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger A. T. et.al.structure calculation
SparkyGoddardchemical shift assignment
PIPPGarrettpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 43 / 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