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(-) Description

Title :  CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C16-CERAMIDE (P212121)
 
Authors :  N. Kudo, K. Kumagai, S. Wakatsuki, M. Nishijima, K. Hanada, R. Kato
Date :  28 Nov 06  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipid Transfer Protein, Cert, Ceramide Transfer, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kudo, K. Kumagai, N. Tomishige, T. Yamaji, S. Wakatsuki, M. Nishijima, K. Hanada, R. Kato
Structural Basis For Specific Lipid Recognition By Cert Responsible For Nonvesicular Trafficking Of Ceramide.
Proc. Natl. Acad. Sci. Usa V. 105 488 2008
PubMed-ID: 18184806  |  Reference-DOI: 10.1073/PNAS.0709191105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPID-TRANSFER PROTEIN CERT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-5X1 (MODIFIED)
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCERT START DOMAIN (RESIDUES 347-598)
    GeneCERT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOODPASTURE-ANTIGEN BINDING PROTEIN, GPBP, CDNA FLJ34532 FIS, CLONE HLUNG2008235, HIGHLY SIMILAR TO HOMO SAPIENS GOODPASTURE ANTIGEN-BINDING PROTEIN (COL4A3BP)MRNA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
116C1Ligand/IonN-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
2DMS2Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:436 , ARG A:442 , GLU A:446 , GLN A:467 , HIS A:469 , VAL A:472 , ALA A:475 , TYR A:482 , ASN A:504 , VAL A:525 , TYR A:553 , LEU A:568 , VAL A:571 , GLU A:575 , TYR A:576 , PHE A:579 , HOH A:766BINDING SITE FOR RESIDUE 16C A 600
2AC2SOFTWAREGLN A:384 , ASP A:385 , VAL A:386 , TYR A:404 , LYS A:419BINDING SITE FOR RESIDUE DMS A 701
3AC3SOFTWAREILE A:528 , GLN A:530 , LYS A:550 , ILE A:551 , THR A:552 , HOH A:788BINDING SITE FOR RESIDUE DMS A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E3O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061815K599RC43BP_HUMANPolymorphism55882089AK573R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STARTPS50848 START domain profile.C43BP_HUMAN415-618  1A:389-592

(-) Exons   (0, 0)

(no "Exon" information available for 2E3O)

(-) 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:231
 aligned with C43BP_HUMAN | Q9Y5P4 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:260
                                   374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624
          C43BP_HUMAN   365 HRFVQKPYSRSSSMSSIDLVSASDDVHRFSSQVEEMVQNHMTYSLQDVGGDANWQLVVEEGEMKVYRREVEENGIVLDPLKATHAVKGVTGHEVCNYFWNVDVRNDWETTIENFHVVETLADNAIIIYQTHKRVWPASQRDVLYLSVIRKIPALTENDPETWIVCNFSVDHDSAPLNNRCVRAKINVAMICQTLVSPPEGNQEISRDNILCKITYVANVNPGGWAPASVLRAVAKREYPKFLKRFTSYVQEKTAGKPILF 624
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh--------------------------hhhhhhhhhhhh.........eeeeeee..eeeeee..ee..ee...eeeeeeee..hhhhhhhhhhh..hhhhhh..eeeeeeeeeee..eeeeeeee........eeeeeeeeeeee.........eeeeeeee............ee.eeeeeeeeeeee...---...hhh.eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------START  PDB: A:389-592 UniProt: 415-618                                                                                                                                                                      ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e3o A 365 HRFVQK--------------------------VEEMVQNHMTYSLQDVGGDANWQLVVEEGEMKVYRREVEENGIVLDPLKATHAVKGVTGHEVCNYFWNVDVRNDWETTIENFHVVETLADNAIIIYQTHKRVWPASQRDVLYLSVIRKIPALTENDPETWIVCNFSVDHDSAPLNNRCVRAKINVAMICQTLVSPP---QEISRDNILCKITYVANVNPGGWAPASVLRAVAKREYPKFLKRFTSYVQEKTAGKPILF 598
                                 |   -         -         -  |    378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       | - |     548       558       568       578       588       598
                               370                        371                                                                                                                                                                  536 540                                                          

   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 2E3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E3O)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C43BP_HUMAN | Q9Y5P4)
molecular function
    GO:0097001    ceramide binding    Interacting selectively and non-covalently with any ceramide, a class of lipids that is composed of sphingosine linked to a fatty acid. Ceramides are a major component of cell membranes.
    GO:0035620    ceramide transporter activity    Enables the directed movement of ceramides into, out of or within a cell, or between cells. Ceramides are a class of lipid composed of sphingosine linked to a fatty acid.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
biological process
    GO:0035621    ER to Golgi ceramide transport    The directed movement of a ceramide from the endoplasmic reticulum (ER) to the Golgi. Ceramides are a class of lipid composed of sphingosine linked to a fatty acid.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006672    ceramide metabolic process    The chemical reactions and pathways involving ceramides, any N-acylated sphingoid.
    GO:0007029    endoplasmic reticulum organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0070584    mitochondrion morphogenesis    The process in which the anatomical structures of a mitochondrion are generated and organized.
    GO:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0034976    response to endoplasmic reticulum stress    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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0030148    sphingolipid biosynthetic process    The chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        C43BP_HUMAN | Q9Y5P42e3m 2e3n 2e3p 2e3q 2e3r 2e3s 2rsg 2z9y 2z9z 3h3q 3h3r 3h3s 3h3t 4hhv 5jjd

(-) Related Entries Specified in the PDB File

2e3m 2e3n 2e3p 2e3q 2e3r 2e3s