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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMODIMERIC MAFB IN COMPLEX WITH THE T-MARE BINDING SITE
 
Authors :  L. Consani Textor, S. Holton, M. Wilmanns
Date :  25 Sep 09  (Deposition) - 08 Dec 10  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Repressor, Dna-Binding, Transcription, Proto-Oncogene, Transcription Regulation, Tumor Suppressor, Dna, B-Zip, Nucleus, Activator, Ap-1 Binding Site, Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Pogenberg, L. Consani Textor, L. Vanhille, S. J. Holton, M. H. Sieweke, M. Wilmanns
Design Of A Bzip Transcription Factor With Homo/Heterodimer Induced Dna-Binding Preference.
Structure V. 22 466 2014
PubMed-ID: 24530283  |  Reference-DOI: 10.1016/J.STR.2013.12.017

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR MAFB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS-RIL
    Fragment: RESIDUES 211-306
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG B, TRANSCRIPTION FACTOR MAF-1, SEGMENTATION PROTEIN KR, KREISLER, MAF-B
 
Molecule 2 - DNA (5'-D(*TP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP *GP*CP*AP*AP*AP*T)-3')
    Chains: C
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Synonym: T-MARE BINDING SITE
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*TP*TP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP *GP*CP*AP*AP*TP*T)-3')
    Chains: D
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Synonym: T-MARE BINDING SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:265 , DT D:2BINDING SITE FOR RESIDUE MG D 20

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WTY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:212 -Asp A:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.MAFB_MOUSE238-301
 		  2A:238-301
B:238-301

(-) Exons   (0, 0)

(no "Exon" information available for 2WTY)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:94
 aligned with MAFB_MOUSE | P54841 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:94
                                   221       231       241       251       261       271       281       291       301    
           MAFB_MOUSE   212 SDDQLVSMSVRELNRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKCEKLANSG 305
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------BZIP  PDB: A:238-301 UniProt: 238-301                           ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2wty A 212 SDDQLVSMSVRELNRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKLANSG 305
                                   221       231       241       251       261       271       281       291       301    


Chain B from PDB  Type:PROTEIN  Length:97
 aligned with MAFB_MOUSE | P54841 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:98
                                   219       229       239       249       259       269       279       289       299        
           MAFB_MOUSE   210 RFSDDQLVSMSVRELNRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKCEKLANSGFR 307
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -bZIP_Maf-2wtyB01 B:211-303                                                                   ---- Pfam domains (1)
           Pfam domains (2) -bZIP_Maf-2wtyB02 B:211-303                                                                   ---- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------BZIP  PDB: B:238-301 UniProt: 238-301                           ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2wty B 210 MFSDDQLVSMSVRELNRHLRGFTKDEVIRLKQKRRTLKNRGYAQSCRYKRVQQKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKLANSG-R 306
                                   219       229       239       249       259       269       279       289       299     | |
                                                                                                                         305 |
                                                                                                                           306


Chain C from PDB  Type:DNA  Length:20
                                                    
                 2wty C   0 TAATTGCTGACTCAGCAAAT  19
                                     9        19


Chain D from PDB  Type:DNA  Length:19
                                                   
                 2wty D   1 ATTTGCTGAGTCAGCAATT  19
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 2WTY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: bZIP (54)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MAFB_MOUSE | P54841)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0035284    brain segmentation    Division of the brain into a series of semi-repetitive parts or segments.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0045647    negative regulation of erythrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
    GO:0045671    negative regulation of osteoclast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
    GO:0021571    rhombomere 5 development    The process whose specific outcome is the progression of rhombomere 5 over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order.
    GO:0021572    rhombomere 6 development    The process whose specific outcome is the progression of rhombomere 6 over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order.
    GO:0007379    segment specification    The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    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: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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MAFB_MOUSE | P54841: 2wt7 4auw

(-) Related Entries Specified in the PDB File

2wt7 CRYSTAL STRUCTURE OF THE BZIP HETERODIMERIC COMPLEX MAFB:CFOS BOUND TO DNA