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(-) Description

Title :  CRYSTAL STRUCTURE OF GOLGI PHOSPHOPROTEIN 3 N-TERM TRUNCATION VARIANT
 
Authors :  K. R. Schmitz, N. J. Bessman, T. G. Setty, K. M. Ferguson
Date :  11 Nov 09  (Deposition) - 15 Dec 09  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (24x)
Keywords :  Beta Hairpin, Phosphoinositide Binding Domain, Cell Membrane, Cytoplasm, Endosome, Golgi Apparatus, Membrane, Mitochondrion, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Wood, K. R. Schmitz, N. J. Bessman, T. G. Setty, K. M. Ferguson, C. G. Burd
Ptdins4P Recognition By Vps74/Golph3 Links Ptdins 4-Kinase Signaling To Retrograde Golgi Trafficking.
J. Cell Biol. V. 187 967 2009
PubMed-ID: 20026658  |  Reference-DOI: 10.1083/JCB.200909063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GOLGI PHOSPHOPROTEIN 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System StrainB834(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 52-298
    GeneGOLPH3, GPP34
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOAT PROTEIN GPP34, MITOCHONDRIAL DNA ABSENCE FACTOR, MIDAS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (24x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 264)
No.NameCountTypeFull Name
1MSE120Mod. Amino AcidSELENOMETHIONINE
2SO4144Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , TRP A:81 , ASN A:172 , VAL A:173 , ARG A:174BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWARETHR A:160 , TRP A:161 , ASN A:162BINDING SITE FOR RESIDUE SO4 A 2
3AC3SOFTWAREARG A:100 , ARG A:102BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREARG A:234 , ARG A:235BINDING SITE FOR RESIDUE SO4 A 4
5AC5SOFTWAREASN A:206 , ASN A:208 , ARG A:212BINDING SITE FOR RESIDUE SO4 A 5
6AC6SOFTWARETRP A:225 , ASN A:227 , ARG A:267BINDING SITE FOR RESIDUE SO4 A 6

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:84 -A:108

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KN1)

(-) Exons   (0, 0)

(no "Exon" information available for 3KN1)

(-) 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:239
 aligned with GOLP3_HUMAN | Q9H4A6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:239
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         
          GOLP3_HUMAN    59 RLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVLTTEKQNFLLFDMTTHPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFT 297
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---GPP34-3kn1A01 A:62-292                                                                                                                                                                                                                 ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..eee..............eee.......hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhh....hhhhhhhhhhhhh.....eeeee..eeeee....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn1 A  59 RLTLmEEVLLLGLKDREGYTSFWNDCISSGLRGCmLIELALRGRLQLEACGmRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVLTTEKQNFLLFDmTTHPLTNNNIKQRLIKKVQEAVLDKWVNDPHRmDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFT 297
                                |   68        78        88    |   98       108 |     118       128       138       148       158       168       178       188       198|      208       218       228   |   238       248       258       268       278       288         
                                |                            93-MSE          110-MSE                                                                                  199-MSE                          232-MSE                                                             
                               63-MSE                                                                                                                                                                                                                                      

   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 3KN1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KN1)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)
Chain A   (GOLP3_HUMAN | Q9H4A6)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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).
biological process
    GO:0007030    Golgi organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
    GO:0090161    Golgi ribbon formation    The formation of a continuous ribbon of interconnected Golgi stacks of flat cisternae.
    GO:0043001    Golgi to plasma membrane protein transport    The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane.
    GO:0048194    Golgi vesicle budding    The evagination of the Golgi membrane, resulting in formation of a vesicle.
    GO:0048193    Golgi vesicle transport    The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
    GO:0090164    asymmetric Golgi ribbon formation    The asymmetric formation of a continuous ribbon of interconnected Golgi stacks of flat cisternae that contributes to the establishment of epithelial cell polarity.
    GO:0060352    cell adhesion molecule production    The appearance of a cell adhesion molecule due to biosynthesis or secretion.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0010467    gene expression    The process in which a gene's 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:0009101    glycoprotein biosynthetic process    The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0050901    leukocyte tethering or rolling    Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0032008    positive regulation of TOR signaling    Any process that activates or increases the frequency, rate or extent of TOR signaling.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0045053    protein retention in Golgi apparatus    The retention of proteins within the Golgi apparatus. Golgi-localized carbohydrate-modifying enzymes have a short N-terminal domain that faces the cytosol, a single transmembrane alpha helix, and a large C-terminal domain that faces the Golgi lumen and that contains the catalytic site. How the membrane-spanning alpha helix in a Golgi enzyme causes its localization and prevents its movement to the plasma membrane is not known.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    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:0010821    regulation of mitochondrion organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.
    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:0031985    Golgi cisterna    Any of the thin, flattened membrane-bounded compartments that form the central portion of the Golgi complex.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2zih STRUCTURE OF THE YEAST HOMOLOG, VPS74.
2zii STRUCTURE OF AN N-TERMINAL TRUNCATION OF THE YEAST HOMOLOG, VPS74.