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(-) Description

Title :  N-TERMINAL 3 DOMAINS OF CI-MPR BOUND TO MANNOSE 6-PHOSPHATE
 
Authors :  L. J. Olson, N. M. Dahms, J. -J. P. Kim
Date :  01 Apr 04  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lectin; Receptor; Mannose 6-Phosphate, Protein Transport, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Olson, N. M. Dahms, J. -J. P. Kim
The N-Terminal Carbohydrate Recognition Site Of The Cation-Independent Mannose 6-Phosphate Receptor
J. Biol. Chem. V. 279 34000 2004
PubMed-ID: 15169779  |  Reference-DOI: 10.1074/JBC.M404588200

(-) Compounds

Molecule 1 - CATION-INDEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: 5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: N-TERMINAL 3 DOMAINS
    Gene: IGF2R, M6P
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: CI MAN-6-P RECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL2Ligand/IonGLYCEROL
3M6P2Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:76 , NAG A:502BINDING SITE FOR RESIDUE NDG A 501
02AC2SOFTWARENDG A:501 , BMA A:503BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWARENAG A:502 , NAG B:1501BINDING SITE FOR RESIDUE BMA A 503
04AC4SOFTWAREBMA A:503 , ASN B:1076 , GLN B:1089BINDING SITE FOR RESIDUE NAG B 1501
05AC5SOFTWAREGLU A:116 , GLN A:364 , ASN A:365BINDING SITE FOR RESIDUE NAG A 601
06AC6SOFTWAREARG B:1288 , GLN B:1364 , ASN B:1365 , HOH B:1956 , HOH B:1993 , HOH B:1998BINDING SITE FOR RESIDUE NAG B 1601
07AC7SOFTWARETYR A:324 , GLN A:348 , GLN A:356 , CYS A:385 , SER A:386 , ARG A:391 , GLU A:416 , CYS A:419 , TYR A:421 , HOH A:1745 , HOH A:1828BINDING SITE FOR RESIDUE M6P A 500
08AC8SOFTWARELYS A:350 , HOH A:1846 , TYR B:1324 , GLN B:1348 , GLN B:1356 , CYS B:1385 , SER B:1386 , ARG B:1391 , GLU B:1416 , TYR B:1421 , HOH B:1897 , HOH B:1904 , HOH B:1980BINDING SITE FOR RESIDUE M6P B 1500
09AC9SOFTWARELEU A:198 , ARG A:200 , PHE A:236 , LYS A:265 , CYS A:268BINDING SITE FOR RESIDUE GOL A 4005
10BC1SOFTWARETHR B:1367 , MET B:1392 , HOH B:1728 , HOH B:1834BINDING SITE FOR RESIDUE GOL B 4006

(-) SS Bonds  (23, 23)

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
13B:1013 -B:1033
14B:1041 -B:1048
15B:1096 -B:1123
16B:1136 -B:1174
17B:1190 -B:1197
18B:1237 -B:1268
19B:1250 -B:1280
20B:1290 -B:1331
21B:1339 -B:1347
22B:1385 -B:1419
23B:1399 -B:1431

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SYO)

(-) 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:422
 aligned with MPRI_BOVIN | P08169 from UniProtKB/Swiss-Prot  Length:2499

    Alignment length:426
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
          MPRI_BOVIN     51 AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV  476
               SCOP domains d1syoa1 A:7-129 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                             d1syoa2 A:130-280 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                                                       d1syoa3 A:281-432 Cation-ind    ependent mannose-6-phosphate receptor (MIR-receptor)                                                                     SCOP domains
               CATH domains 1syoA01 A:7-129 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                     1syoA02 A:130-285 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                    1syoA03 A:286-432 Catio    n-dependent Mannose-6-phosphate Receptor; Chain A                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...eeeee....eeeee.......hhhhh..eeeeeee....eeeeeee...eee...eeeeeeeee......eeeeeeeeee......eeeeee...eeeeeeeehhhh.hhhhh.......eee.....eee.hhhh.....ee.......eeeee........................eeeee....ee..ee....ee.....eeeeee......hhhhh....eeeeeee...........eeeehhh.eeeeeee.hhhhhhhhhee...eehhhhhh..ee.hhhhh----....eeee...eeeee.......hhhhh.....eeeee..eeeeeee..eeeeeeeeee..eeeeeee...........eeeeeeee...........eeeeee...eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1syo A    7 AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSR----DSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV  432
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306 |    |316       326       336       346       356       366       376       386       396       406       416       426      
                                                                                                                                                                                                                                                                                                                                       308  313                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:408
 aligned with MPRI_BOVIN | P08169 from UniProtKB/Swiss-Prot  Length:2499

    Alignment length:426
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
          MPRI_BOVIN     51 AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV  476
               SCOP domains d1syob1 B:1007-1129 Cation-independent mannose-6-phosphate receptor (MIR-r       eceptor)                                  d1syob2 B:1130-1280 Cation-independent mannose-6-phosphate receptor (MIR-receptor)                                                                     d1syob3 B:1281-1432 Cation-in    dependent mannose-6-phosphate receptor (MIR-receptor)                                                                   SCOP domains
               CATH domains 1syoB01 B:1007-1129 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                 1syoB02 B:1130-1285 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                  1syoB03 B:1286-1432 Cati    on-dependent Mannose-6-phosphate Receptor; Chain A                                                                      CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB01 B:1388-1432                      Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB02 B:1388-1432                      Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB03 B:1388-1432                      Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB04 B:1388-1432                      Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB05 B:1388-1432                      Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CIMR-1syoB06 B:1388-1432                      Pfam domains (6)
         Sec.struct. author ..hhhhh...eeeee....eeeee..............eeeeeee....eeeeeee...eeee..eeeee....-------.eeeeeeee......eeeeee...eeeeeeeehhhh.............eee.....eee.hhhh.....eee......eeeee............hhhhhh......eeeee..eeeeeeee....eeee..eeeeeee.-------.......eeeeeee...........eeeee...eeeeeee.hhhhhhhh.ee...eehhhhhh..ee.hhhhh.----...eeee...eeeee.......hhhhh.....eeeee......eee......eeeeee..eeeeee............eeeeeeee............eeeeee..eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1syo B 1007 AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFNTTVN-------IQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVK-------FCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRV----SLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACV 1432
                                  1016      1026      1036      1046      1056      1066      1076   |     - |    1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226 |    1236      1246      1256      1266      1276      1286      1296      1306  |   1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      
                                                                                                  1080    1088                                                                                                                                        1228    1236                                                                     1309 1314
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: M6PR (17)
(-)
Family: CIMR (8)
(-)
Bos taurus (Bovine) (5)
1aCIMR-1syoB01B:1388-1432
1bCIMR-1syoB02B:1388-1432
1cCIMR-1syoB03B:1388-1432
1dCIMR-1syoB04B:1388-1432
1eCIMR-1syoB05B:1388-1432
1fCIMR-1syoB06B:1388-1432

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | P08169: 1q25 1sz0 2kva 2kvb

(-) Related Entries Specified in the PDB File

1q25 N-TERMINAL 3 DOMAINS OF THE CATION INDEPENDENT MANNOSE 6- PHOSPHATE RECEPTOR
1sz0