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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER, 40 STRUCTURES
 
Authors :  P. Lavigne, M. P. Crump, S. M. Gagne, R. S. Hodges, C. M. Kay, B. D. Sykes
Date :  09 Jun 98  (Deposition) - 27 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (40x)
Keywords :  Leucine Zippers, 2D Nmr, Solution Structure, H-Bonds, Buried Salt Bridge (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Lavigne, M. P. Crump, S. M. Gagne, R. S. Hodges, C. M. Kay, B. D. Sykes
Insights Into The Mechanism Of Heterodimerization From The 1H-Nmr Solution Structure Of The C-Myc-Max Heterodimeric Leucine Zipper.
J. Mol. Biol. V. 281 165 1998
PubMed-ID: 9680483  |  Reference-DOI: 10.1006/JMBI.1998.1914
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER
    Chains: A
    Engineered: YES
    Fragment: LEUCINE ZIPPER
    Other Details: DISULPHIDE LINK AT THE N-TERMINI
    Other Details - Source: 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.
    Synonym: COILED COIL, LZ
    Synthetic: YES
 
Molecule 2 - C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER
    Chains: B
    Engineered: YES
    Fragment: LEUCINE ZIPPER
    Other Details: DISULPHIDE LINK AT THE N-TERMINI
    Other Details - Source: 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.
    Synonym: COILED COIL, LZ
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (40x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

NMR Structure (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NH22Mod. Amino AcidAMINO GROUP

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC3SOFTWARELEU A:34BINDING SITE FOR RESIDUE NH2 A 35
2AC4SOFTWARELEU B:34BINDING SITE FOR RESIDUE NH2 B 35

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:3 -B:3

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A93)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A93)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BHLHPS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile.MYC_HUMAN354-406  1A:6-6

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003779701cENSE00001852283chr8:128748330-128748869540MYC_HUMAN1-10100--
1.2aENST000003779702aENSE00001626023chr8:128750494-128751265772MYC_HUMAN11-2682580--
1.3bENST000003779703bENSE00000926396chr8:128752642-1287536741033MYC_HUMAN268-4541871A:2-35 (gaps)95

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:34
 aligned with MYC_HUMAN | P01106 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:95
                                   350       360       370       380       390       400       410       420       430     
            MYC_HUMAN   341 KCTSPRSSDTEENVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQLR 435
               SCOP domains d2a9                                                             3a_ A: C-myc                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------BHLH  PDB: A:6-6 UniProt: 354-406                    ----------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:2-35 (gaps) UniProt: 268-454 [INCOMPLETE]                                     Transcript 1
                 2a93 A   2 xCGG-------------------------------------------------------------VQAEEQKLISEEDLLRKRREQLKHKLEQLx  35
                            |  |     -         -         -         -         -         -     |  10        20        30    |
                            |  5                                                             6                           35-NH2
                            2-ACE                                                                                          


Chain B from PDB  Type:PROTEIN  Length:34
 aligned with MAX_MOUSE | P28574 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:52
                                    61        71        81        91       101  
            MAX_MOUSE    52 SLQGEKASRAQILDKATEYIQYMRRKNDTHQQDIDDLKRQNALLEQQVRALE 103
               SCOP domains d2a9                  3b_ B: Max                     SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ....------------------hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 2a93 B   2 xCGG------------------MRRKNDTHQQDIDDLKRQNALLEQQVRALx  35
                            |  |     -         -  |     13        23        33 |
                            |  5                  6                           35-NH2
                            2-ACE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

NMR Structure
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A93)

(-) Gene Ontology  (58, 65)

NMR Structure(hide GO term definitions)
Chain A   (MYC_HUMAN | P01106)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070888    E-box binding    Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0001658    branching involved in ureteric bud morphogenesis    The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034644    cellular response to UV    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0051276    chromosome organization    A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
    GO:0006112    energy reserve metabolic process    The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
    GO:0044346    fibroblast apoptotic process    Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0051782    negative regulation of cell division    Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0045656    negative regulation of monocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation.
    GO:0032873    negative regulation of stress-activated MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:2000573    positive regulation of DNA biosynthetic process    Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0048146    positive regulation of fibroblast proliferation    Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0002053    positive regulation of mesenchymal cell proliferation    The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
    GO:0090096    positive regulation of metanephric cap mesenchymal cell proliferation    Any process that increases the frequency, rate, or extent of metanephric cap mesenchymal cell proliferation. Metanephric cap mesenchymal cell proliferation is the multiplication or reproduction of metanephric cap mesenchymal cells, resulting in the expansion of the cell population. A metanephric cap mesenchymal cell is a mesenchymal cell that has condensed with other mesenchymal cells surrounding the ureteric bud tip.
    GO:2001022    positive regulation of response to DNA damage stimulus    Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032204    regulation of telomere maintenance    Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0070848    response to growth factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Chain B   (MAX_MOUSE | P28574)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  MAX_MOUSE | P28574
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  MYC_HUMAN | P01106
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MAX_MOUSE | P28574: 1a93 3u5v
        MYC_HUMAN | P01106: 1a93 1ee4 1mv0 1nkp 2or9 4y7r 5i4z 5i50

(-) Related Entries Specified in the PDB File

1a93