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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL 3 DOMAINS OF CI-MPR
 
Authors :  L. J. Olson, N. M. Dahms, J. -J. P. Kim
Date :  23 Jul 03  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Lectin, Receptor, Mannose 6-Phosphate, Protein Transport, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Olson, R. D. Yammani, N. M. Dahms, J. -J. P. Kim
Structure Of Upar, Plasminogen, And Sugar-Binding Sites Of The 300 Kda Mannose 6-Phosphate Receptor
Embo J. V. 23 2019 2004
PubMed-ID: 15085180  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600215

(-) Compounds

Molecule 1 - CATION-INDEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell5B1-4 CELLS
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentN-TERMINAL 3 DOMAINS
    GeneIGF2R
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymCI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:323 , TYR A:324 , LYS A:350 , HOH A:630 , BMA A:1005BINDING SITE FOR RESIDUE MAN A 1003
2AC2SOFTWAREGLN A:348 , ARG A:391 , GLU A:416 , CYS A:419 , TYR A:421 , BMA A:1005 , GOL A:4005BINDING SITE FOR RESIDUE MAN A 1004
3AC3SOFTWARETYR A:324 , LYS A:350 , HOH A:639 , HOH A:693 , HOH A:711 , NAG A:1002 , MAN A:1003 , MAN A:1004BINDING SITE FOR RESIDUE BMA A 1005
4AC4SOFTWARETHR A:67 , GLU A:74 , ASN A:76 , GLN A:89 , HOH A:628 , HOH A:691 , HOH A:809 , HOH A:923 , NAG A:1002BINDING SITE FOR RESIDUE NAG A 1001
5AC5SOFTWAREHOH A:693 , HOH A:816 , HOH A:901 , HOH A:965 , NAG A:1001 , BMA A:1005BINDING SITE FOR RESIDUE NAG A 1002
6AC6SOFTWAREGLN A:364 , ASN A:365 , HOH A:782 , HOH A:823 , HOH A:844 , HOH A:907 , NAG A:2002BINDING SITE FOR RESIDUE NAG A 2001
7AC7SOFTWARENAG A:2001BINDING SITE FOR RESIDUE NAG A 2002
8AC8SOFTWAREGLU A:416 , ASP A:418 , HOH A:890 , HOH A:908 , MAN A:1004BINDING SITE FOR RESIDUE GOL A 4005

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:13 -A:33
2A:41 -A:48
3A:81 -A:111
4A:96 -A:123
5A:136 -A:174
6A:190 -A:197
7A:237 -A:268
8A:250 -A:280
9A:290 -A:331
10A:339 -A:347
11A:385 -A:419
12A:399 -A:431

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q25)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q25)

(-) 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:428
 aligned with MPRI_BOVIN | P08169 from UniProtKB/Swiss-Prot  Length:2499

    Alignment length:428
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468        
           MPRI_BOVIN    49 QGAEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV 476
               SCOP domains --d1q25a1 A:7-129 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                             d1q25a2 A:130-280 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                                                       d1q25a3 A:281-432 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                                                         SCOP domains
               CATH domains 1q25A01 A:5-129 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                       1q25A02 A:130-285 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                    1q25A03 A:286-432 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                            CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1q25A01 A:388-432                        Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1q25A02 A:388-432                        Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1q25A03 A:388-432                        Pfam domains (3)
         Sec.struct. author ....hhhhh...eeeeehhh.eeeee..............eeeeeee....eeeeeee...eeee..eeeeeeeee......eeeeeeeeee......eeeeee...eeeeeeeehhhh.hhhhh.......eee.....eee.hhhh.....ee........eeee..............hhhhh.....eeee....eeeeeee....eeee..eeeeeee...............eeeeeee...........eeeee...eeeeeee.hhhhhhhh.ee...eehhhhhh..ee.hhhh.........eeee...eeeee.......hhhhh.....eeeee......eee......eeeeee..eeeeee............eeeeeeee............eeeeee..eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q25 A   5 QGAEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV 432
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        

   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  (1, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: M6PR (17)
(-)
Family: CIMR (8)
1aCIMR-1q25A01A:388-432
1bCIMR-1q25A02A:388-432
1cCIMR-1q25A03A:388-432

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MPRI_BOVIN | P08169)
molecular function
    GO:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    GO:0036143    kringle domain binding    Interacting selectively and non-covalently with a kringle domain. Kringle domains are protein domains that fold into large loops stabilized by 3 disulfide linkages, and are important in protein-protein interactions with blood coagulation factors.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

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

UniProtKB/Swiss-Prot
        MPRI_BOVIN | P081691syo 1sz0 2kva 2kvb

(-) Related Entries Specified in the PDB File

1syo 1sz0