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(-) Description

Title :  CRYSTAL STRUCTURE OF MAD-MAX RECOGNIZING DNA
 
Authors :  S. K. Nair, S. K. Burley
Date :  07 Jan 03  (Deposition) - 04 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,D,E,F,G,H,J
Biol. Unit 1:  A,B,F,G  (1x)
Biol. Unit 2:  D,E,H,J  (1x)
Keywords :  Transcription Factor, Dna, Bhlhz, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Nair, S. K. Burley
X-Ray Structures Of Myc-Max And Mad-Max Recognizing Dna: Molecular Bases Of Regulation By Proto-Oncogenic Transcription Factors
Cell(Cambridge, Mass. ) V. 112 193 2003
PubMed-ID: 12553908  |  Reference-DOI: 10.1016/S0092-8674(02)01284-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)- 3'
    Chains: F, G, H, J
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - MAD PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: BHLHZ REGION
    Gene: MAD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAX DIMERIZER
 
Molecule 3 - MAX PROTEIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET 3
    Expression System Vector Type: PLASMID
    Fragment: BHLHZ REGION
    Gene: MAX
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABDEFGHJ
Biological Unit 1 (1x): AB  FG  
Biological Unit 2 (1x):   DE  HJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NLW)

(-) Sites  (0, 0)

(no "Site" information available for 1NLW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NLW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NLW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NLW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NLW)

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002644444aENSE00001885295chr2:70142203-70142535333MAD1_HUMAN1-25250--
1.5aENST000002644445aENSE00001646891chr2:70143253-70143352100MAD1_HUMAN25-58342A:2-3
D:502-503		2
2
1.6ENST000002644446ENSE00001006489chr2:70148868-7014889730MAD1_HUMAN58-68112A:3-13
D:503-513		11
11
1.7ENST000002644447ENSE00000759552chr2:70162483-70162597115MAD1_HUMAN68-106392A:13-51
D:513-551		39
39
1.8bENST000002644448bENSE00000759553chr2:70164367-70164526160MAD1_HUMAN107-160542A:52-80
D:552-578		29
27
1.9cENST000002644449cENSE00000846481chr2:70165229-701700774849MAD1_HUMAN160-221620--
2.1dENST000003586641dENSE00001956202chr14:65569188-65569022167MAX_HUMAN1-12120--
2.3bENST000003586643bENSE00001013639chr14:65568290-6556826427MAX_HUMAN13-2190--
2.4ENST000003586644ENSE00000941006chr14:65560533-65560426108MAX_HUMAN22-57362B:203-236
E:705-736		34
32
2.6aENST000003586646aENSE00001364326chr14:65544754-65544631124MAX_HUMAN58-99422B:237-278
E:737-778		42
42
2.6fENST000003586646fENSE00001884996chr14:65543381-655422621120MAX_HUMAN99-160622B:278-278
E:778-778		1
1

(-) Sequences/Alignments

Asymmetric 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:79
 aligned with MAD1_HUMAN | Q05195 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:79
                                    66        76        86        96       106       116       126         
           MAD1_HUMAN    57 SRSTHNEMEKNRRAHLRLCLEKLKGLVPLGPESSRHTTLSLLTKAKLHIKKLEDCDRKAVHQIDQLQREQRHLKRQLEK 135
               SCOP domains d1nlwa_ A: Mad protein                                                          SCOP domains
               CATH domains 1nlwA00 A:2-80 MYOD Basic-Helix-Loop-Helix Domain, subunit B                    CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.---------Exon 1.7  PDB: A:13-51 UniProt: 68-106 Exon 1.8b  PDB: A:52-80       Transcript 1 (1)
           Transcript 1 (2) -Exon 1.6   ------------------------------------------------------------------- Transcript 1 (2)
                 1nlw A   2 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLEK  80
                                    11        21        31        41        51        61        71         


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with MAX_HUMAN | P61244 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:76
                                    33        43        53        63        73        83        93      
            MAX_HUMAN    24 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV  99
               SCOP domains d1nlwb_ B: Max protein                                                       SCOP domains
               CATH domains 1nlwB00 B:203-278 MYOD Basic-Helix-Loop-Helix Domain, subunit B              CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4  PDB: B:203-236          Exon 2.6a  PDB: B:237-278 UniProt: 58-99   Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------------------2 Transcript 2 (2)
                 1nlw B 203 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV 278
                                   212       222       232       242       252       262       272      


Chain D from PDB  Type:PROTEIN  Length:77
 aligned with MAD1_HUMAN | Q05195 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:77
                                    66        76        86        96       106       116       126       
           MAD1_HUMAN    57 SRSTHNEMEKNRRAHLRLCLEKLKGLVPLGPESSRHTTLSLLTKAKLHIKKLEDCDRKAVHQIDQLQREQRHLKRQL 133
               SCOP domains d1nlwd_ D: Mad protein                                                        SCOP domains
               CATH domains 1nlwD00 D:502-578 MYOD Basic-Helix-Loop-Helix Domain, subunit B               CATH domains
           Pfam domains (1) HLH-1nlwD01 D:502-554                                ------------------------ Pfam domains (1)
           Pfam domains (2) HLH-1nlwD02 D:502-554                                ------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.---------Exon 1.7  PDB: D:513-551               Exon 1.8b  PDB: D:552-578   Transcript 1 (1)
           Transcript 1 (2) -Exon 1.6   ----------------------------------------------------------------- Transcript 1 (2)
                 1nlw D 502 SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQL 578
                                   511       521       531       541       551       561       571       


Chain E from PDB  Type:PROTEIN  Length:74
 aligned with MAX_HUMAN | P61244 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:74
                                    35        45        55        65        75        85        95    
            MAX_HUMAN    26 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV  99
               SCOP domains d1nlwe_ E: Max protein                                                     SCOP domains
               CATH domains 1nlwE00 E:705-778 MYOD Basic-Helix-Loop-Helix Domain, subunit B            CATH domains
           Pfam domains (1) HLH-1nlwE01 E:705-754                             ------------------------ Pfam domains (1)
           Pfam domains (2) HLH-1nlwE02 E:705-754                             ------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.4  PDB: E:705-736        Exon 2.6a  PDB: E:737-778 UniProt: 58-99   Transcript 2 (1)
           Transcript 2 (2) -------------------------------------------------------------------------2 Transcript 2 (2)
                 1nlw E 705 AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV 778
                                   714       724       734       744       754       764       774    


Chain F from PDB  Type:DNA  Length:18
                                                  
                 1nlw F 102 GAGTAGCACGTGCTACTC 119
                                   111        


Chain G from PDB  Type:DNA  Length:18
                                                  
                 1nlw G 302 GAGTAGCACGTGCTACTC 319
                                   311        


Chain H from PDB  Type:DNA  Length:18
                                                  
                 1nlw H 602 GAGTAGCACGTGCTACTC 619
                                   611        


Chain J from PDB  Type:DNA  Length:18
                                                  
                 1nlw J 802 GAGTAGCACGTGCTACTC 819
                                   811
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: HLH] (6)
(-)
Family: HLH (6)
(-)
Homo sapiens (Human) (4)
1aHLH-1nlwD01D:502-554
1bHLH-1nlwD02D:502-554
1cHLH-1nlwE01E:705-754
1dHLH-1nlwE02E:705-754

(-) Gene Ontology  (38, 47)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (MAD1_HUMAN | Q05195)
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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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:0001078    transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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: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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.

Chain B,E   (MAX_HUMAN | P61244)
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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0000983    transcription factor activity, RNA polymerase II core promoter sequence-specific    Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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.
biological process
    GO:0071375    cellular response to peptide hormone 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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0009267    cellular response to starvation    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 deprivation of nourishment.
    GO:0010629    negative regulation of gene expression    Any process that decreases 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:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    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:0048678    response to axon injury    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 an axon injury stimulus.
    GO:0032868    response to insulin    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0010243    response to organonitrogen compound    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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    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: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:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    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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  1nlw
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  MAD1_HUMAN | Q05195
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  MAX_HUMAN | P61244
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Access by UniProt ID/Accession number
  MAD1_HUMAN | Q05195
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MAX_HUMAN | P61244
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MAD1_HUMAN | Q05195: 1e91 1g1e 1pd7 1s5q
        MAX_HUMAN | P61244: 1an2 1hlo 1nkp 1r05 5eyo

(-) Related Entries Specified in the PDB File

1nkp CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA