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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  HUMAN NAC DIMERIZATION DOMAIN
 
Authors :  Y. Liu, Y. Hu, X. Li, L. Niu, M. Teng
Date :  28 Jan 10  (Deposition) - 23 Mar 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Barrel, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Liu, Y. Hu, X. Li, L. Niu, M. Teng
The Crystal Structure Of The Human Nascent Polypeptide-Associated Complex Domain Reveals A Nucleic Acid-Binding Region On The Naca Subunit
Biochemistry V. 49 2890 2010
PubMed-ID: 20214399  |  Reference-DOI: 10.1021/BI902050P

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR BTF3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 97-162
    GeneNACA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRNA POLYMERASE B TRANSCRIPTION FACTOR 3
 
Molecule 2 - NASCENT POLYPEPTIDE-ASSOCIATED COMPLEX SUBUNIT ALPHA
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 84-136
    GeneBTF3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNAC-ALPHA, ALPHA-NAC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3LKX)

(-) Sites  (0, 0)

(no "Site" information available for 3LKX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LKX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LKX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LKX)

(-) Exons   (0, 0)

(no "Exon" information available for 3LKX)

(-) 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:65
 aligned with BTF3_HUMAN | P20290 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:66
                                   106       116       126       136       146       156      
           BTF3_HUMAN    97 VNNISGIEEVNMFTNQGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSL 162
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains NAC-3lkxA01 A:25-70                           -------------------- Pfam domains
         Sec.struct. author .ee...eeeeeeee...eeeeee..eeeee.-..eeeee..eeeee.hhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 3lkx A  25 VNNISGIEEVNMFTNQGTVIHFNNPKVQASL-ANTFTITGHAETKQLTEMLPSILNQLGADSLTSL  90
                                    34        44        54| |     64        74        84      
                                                         55 |                                 
                                                           57                                 

Chain B from PDB  Type:PROTEIN  Length:54
 aligned with NACA_HUMAN | Q13765 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:54
                                    92       102       112       122       132    
           NACA_HUMAN    83 LGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQ 136
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains -NAC-3lkxB01 B:25-71                            ------ Pfam domains
         Sec.struct. author ...eee..eeeeeeee...eeeeee..eeee.....eeeee...eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3lkx B  24 EGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQ  77
                                    33        43        53        63        73    

   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 3LKX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LKX)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (24, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BTF3_HUMAN | P20290)
molecular function
    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).
biological process
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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   (NACA_HUMAN | Q13765)
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: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.
biological process
    GO:0003231    cardiac ventricle development    The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
    GO:0061384    heart trabecula morphogenesis    The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.
    GO:0010664    negative regulation of striated muscle cell apoptotic process    Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
    GO:1901227    negative regulation of transcription from RNA polymerase II promoter involved in heart development    Any negative regulation of transcription from RNA polymerase II promoter that is involved in heart development.
    GO:2000138    positive regulation of cell proliferation involved in heart morphogenesis    Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis.
    GO:0048633    positive regulation of skeletal muscle tissue growth    Any process that activates, maintains or increases the rate of skeletal muscle growth.
    GO:1901228    positive regulation of transcription from RNA polymerase II promoter involved in heart development    Any positive regulation of transcription from RNA polymerase II promoter that is involved in heart development.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0048742    regulation of skeletal muscle fiber development    Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0043403    skeletal muscle tissue regeneration    The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005854    nascent polypeptide-associated complex    A heterodimeric protein complex that can reversibly bind to ribosomes, and is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome.
    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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    Leu A:75 - Pro A:76   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        BTF3_HUMAN | P202903mcb
        NACA_HUMAN | Q137653mcb 3mce

(-) Related Entries Specified in the PDB File

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