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(-) Description

Title :  PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX
 
Authors :  D. E. Piper, A. H. Batchelor, C. -P. Chang, M. L. Cleary, C. Wolberger
Date :  27 Jan 99  (Deposition) - 19 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Homeodomain, Dna, Complex, Dna-Binding Protein, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Piper, A. H. Batchelor, C. P. Chang, M. L. Cleary, C. Wolberger
Structure Of A Hoxb1-Pbx1 Heterodimer Bound To Dna: Role Of The Hexapeptide And A Fourth Homeodomain Helix In Complex Formation.
Cell(Cambridge, Mass. ) V. 96 587 1999
PubMed-ID: 10052460  |  Reference-DOI: 10.1016/S0092-8674(00)80662-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP *G)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP *G)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (HOMEOBOX PROTEIN HOX-B1)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: HOXB-1
    Expression System Plasmid: PET11-D T7 PROMOTER
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: HEXAPEPTIDE, HOMEODOMAIN
    Gene: HOXB-1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - PROTEIN (PBX1)
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PBX1
    Expression System Plasmid: PET11-D T7 PROMOTER
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: HOMEODOMAIN
    Gene: PBX1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1B72)

(-) Sites  (0, 0)

(no "Site" information available for 1B72)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_068723R207CHXB1_HUMANDisease (HCFP3)387907239AR207C
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HXB1_HUMAN201-261  1A:206-261
2HOMEOBOX_1PS00027 'Homeobox' domain signature.HXB1_HUMAN236-259  1A:236-259
PBX1_HUMAN269-292  1B:269-292

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002391741ENSE00000812623chr17:46608359-46607690670HXB1_HUMAN1-1931931A:177-1859
1.2ENST000002391742ENSE00001315080chr17:46607237-46606797441HXB1_HUMAN193-3011091A:206-26459

(-) 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:68
 aligned with HXB1_HUMAN | P14653 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:88
                                   186       196       206       216       226       236       246       256        
           HXB1_HUMAN   177 ARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 264
               SCOP domains d1b72a_ A                    : Homeobox protein hox-b1                                   SCOP domains
               CATH domains 1b72A00 A                    :177-264 Homeodomain-like                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.--------------------......hhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------C--------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------HOMEOBOX_2  PDB: A:206-261 UniProt: 201-261                  --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------HOMEOBOX_1              ----- PROSITE (2)
           Transcript 1 (1) Exon 1.1         ----------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.2  PDB: A:206-264 UniProt: 193-301 [INCOMPLETE]                   Transcript 1 (2)
                 1b72 A 177 ARTFDWMKV--------------------LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 264
                                    |-         -       206       216       226       236       246       256        
                                  185                  206                                                          


Chain B from PDB  Type:PROTEIN  Length:73
 aligned with PBX1_HUMAN | P40424 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:73
                                   244       254       264       274       284       294       304   
           PBX1_HUMAN   235 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAA 307
               SCOP domains d1b72b_ B: pbx1                                                           SCOP domains
               CATH domains 1b72B00 B:235-307 Homeodomain-like                                        CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------HOMEOBOX_1              --------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 1b72 B 235 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAA 307
                                   244       254       264       274       284       294       304   


Chain D from PDB  Type:DNA  Length:20
                                                    
                 1b72 D   1 ACTCTATGATTGATCGGCTG  20
                                    10        20


Chain E from PDB  Type:DNA  Length:20
                                                    
                 1b72 E  21 TCAGCCGATCAATCATAGAG  40
                                    30        40
   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)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B72)

(-) Gene Ontology  (49, 57)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HXB1_HUMAN | P14653)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    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.
biological process
    GO:0048646    anatomical structure formation involved in morphogenesis    The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    GO:0021612    facial nerve structural organization    The process that contributes to the act of creating the structural organization of the facial nerve. This process pertains to the physical shaping of a rudimentary structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities.
    GO:0021754    facial nucleus development    The process whose specific outcome is the progression of the facial nucleus over time, from its formation to the mature structure.
    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:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    GO:0045944    positive regulation of transcription by RNA polymerase II    Any process that activates or increases 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:0021570    rhombomere 4 development    The process whose specific outcome is the progression of rhombomere 4 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: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:0021546    rhombomere development    The process whose specific outcome is the progression of the rhombomere 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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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   (PBX1_HUMAN | P40424)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    DNA-binding transcription factor activity    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
    GO:0000978    RNA polymerase II proximal promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a gene transcribed by RNA polymerase II. The proximal promoter is in cis with and relatively close to the core promoter.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0001077    proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    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:0043433    negative regulation of DNA-binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0010971    positive regulation of G2/M transition of mitotic cell cycle    Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045944    positive regulation of transcription by RNA polymerase II    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009954    proximal/distal pattern formation    The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end).
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0030278    regulation of ossification    Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    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 by RNA polymerase II    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.
    GO:0001655    urogenital system development    The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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  PBX1_HUMAN | P40424
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 Related Entries

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

UniProtKB/Swiss-Prot
        PBX1_HUMAN | P40424: 1puf

(-) Related Entries Specified in the PDB File

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