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- PDB-2a93: NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIP... -

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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 / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance ...Transcriptional Regulation by E2F6 / Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of monocyte differentiation / response to growth factor / response to alkaloid / B cell apoptotic process / transcription regulator activator activity / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / skeletal system morphogenesis / middle ear morphogenesis / cellular response to peptide hormone stimulus / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / rRNA metabolic process / E-box binding / positive regulation of telomere maintenance / skeletal muscle cell differentiation / MLL1 complex / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / response to axon injury / 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 / cellular response to starvation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / MAPK6/MAPK4 signaling / protein-DNA complex / response to insulin / PML body / protein processing / NOTCH1 Intracellular Domain Regulates Transcription / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / cellular response to xenobiotic stimulus / MAPK cascade / retina development in camera-type eye / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / cellular response to hypoxia / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / axon / negative regulation of gene expression / positive regulation of cell population proliferation / dendrite / ubiquitin protein ligase binding
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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.

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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

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NMR measurement

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

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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

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