[English] 日本語
Yorodumi
- PDB-2a93: NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a93
TitleNMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER, 40 STRUCTURES
Components(C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER) x 2
KeywordsLEUCINE ZIPPERS / 2D NMR / SOLUTION STRUCTURE / H-BONDS / BURIED SALT BRIDGE
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process ...Transcriptional Regulation by E2F6 / Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / RNA polymerase II transcription repressor complex / cellular response to interferon-alpha / Binding of TCF/LEF:CTNNB1 to target gene promoters / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / myotube differentiation / negative regulation of transcription initiation by RNA polymerase II / Regulation of CDH1 mRNA translation by microRNAs / negative regulation of cell division / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / B cell apoptotic process / response to alkaloid / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / fibroblast apoptotic process / negative regulation of stress-activated MAPK cascade / Regulation of NFE2L2 gene expression / protein-DNA complex disassembly / positive regulation of mesenchymal cell proliferation / regulation of telomere maintenance / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / middle ear morphogenesis / rRNA metabolic process / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / E-box binding / positive regulation of telomere maintenance / MLL1 complex / skeletal muscle cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / protein processing / protein-DNA complex / MAPK6/MAPK4 signaling / PML body / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to xenobiotic stimulus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / spindle / RNA polymerase II transcription regulator complex / positive regulation of fibroblast proliferation / Wnt signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / cellular response to UV / MAPK cascade / regulation of gene expression / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / transcription by RNA polymerase II / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of gene expression / axon / positive regulation of cell population proliferation / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
Myc proto-oncogene protein / Protein max
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsLavigne, P. / Crump, M.P. / Gagne, S.M. / Hodges, R.S. / Kay, C.M. / Sykes, B.D.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper.
Authors: Lavigne, P. / Crump, M.P. / Gagne, S.M. / Hodges, R.S. / Kay, C.M. / Sykes, B.D.
History
DepositionJun 9, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / 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_database_status.process_site / _pdbx_nmr_exptl_sample_conditions.pressure_units / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_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 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER
B: C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER


Theoretical massNumber of molelcules
Total (without water)7,6202
Polymers7,6202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40LEAST RESTRAINT VIOLATION ONLY.
Representative

-
Components

#1: Protein/peptide C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER / COILED COIL / LZ


Mass: 3837.432 Da / Num. of mol.: 1 / Fragment: LEUCINE ZIPPER / Source method: obtained synthetically
Details: BOTH C-MYC AND MAX HAVE A NON BIOLOGICAL CGG LINKER AT THE N-TERMINUS OF THE PROTEIN. C-MYC AND MAX ARE NUCLEAR PROTEINS.
References: UniProt: P01106
#2: Protein/peptide C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER / COILED COIL / LZ


Mass: 3782.279 Da / Num. of mol.: 1 / Fragment: LEUCINE ZIPPER / Source method: obtained synthetically
Details: BOTH C-MYC AND MAX HAVE A NON BIOLOGICAL CGG LINKER AT THE N-TERMINUS OF THE PROTEIN. C-MYC AND MAX ARE NUCLEAR PROTEINS.
References: UniProt: P28574
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H 2D NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 100 mM / pH: 4.8 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXR 500VarianVXR 5005001
Varian UNITY 600VarianUNITY 6006002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION ONLY.
Conformers calculated total number: 40 / Conformers submitted total number: 40

+
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