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(-) Description

Title :  CRYSTAL STRUCTURE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR AT PH 7.4
 
Authors :  L. J. Olson, O. Hindsgaul, N. M. Dahms, J. -J. P. Kim
Date :  25 Apr 08  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  P-Type Lectin, Receptor, Mannose 6-Phosphate, Lectin, Glycoprotein, Lysosome, Membrane, Transmembrane, Transport, Protein Transport, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Olson, O. Hindsgaul, N. M. Dahms, J. J. Kim
Structural Insights Into The Mechanism Of Ph-Dependent Ligand Binding And Release By The Cation-Dependent Mannose 6-Phosphate Receptor.
J. Biol. Chem. V. 283 10124 2008
PubMed-ID: 18272523  |  Reference-DOI: 10.1074/JBC.M708994200

(-) Compounds

Molecule 1 - CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneM6PR
    MutationYES
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymCD MAN-6-P RECEPTOR, CD-MPR, 46 KDA MANNOSE 6-PHOSPHATE RECEPTOR, MPR 46

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:79 , ASN A:81 , GLU A:82 , HOH A:4109 , HOH A:4157BINDING SITE FOR RESIDUE NAG A 3001
2AC2SOFTWAREARG A:79 , GLN A:110 , HOH A:4113 , HOH A:4170BINDING SITE FOR RESIDUE NAG A 3002
3AC3SOFTWAREHOH A:4170BINDING SITE FOR RESIDUE MAN A 3005
4AC4SOFTWAREHOH A:4106BINDING SITE FOR RESIDUE MAN A 3003
5AC5SOFTWAREASN B:81 , HOH B:4048BINDING SITE FOR RESIDUE NAG B 4001
6AC9SOFTWAREGLU A:133 , ARG A:135 , HOH A:4017 , HOH A:4032 , HOH A:4051 , LYS B:18BINDING SITE FOR RESIDUE GOL A 4009

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:52
2A:106 -A:141
3A:119 -A:153
4B:6 -B:52
5B:106 -B:141
6B:119 -B:153

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:41 -Pro A:42
2Ser B:41 -Pro B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CY4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CY4)

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000242331ENSBTAE00000295015chr5:108383511-108383668158MPRD_BOVIN1-110--
1.2ENSBTAT000000242332ENSBTAE00000197230chr5:108390145-108390324180MPRD_BOVIN1-61612A:4-33
B:1-33
30
33
1.3ENSBTAT000000242333ENSBTAE00000197232chr5:108391558-108391724167MPRD_BOVIN61-117572A:33-89
B:33-89
57
57
1.4ENSBTAT000000242334ENSBTAE00000295014chr5:108392731-108392840110MPRD_BOVIN117-153372A:89-125
B:89-125
37
37
1.5ENSBTAT000000242335ENSBTAE00000197235chr5:108393267-108393397131MPRD_BOVIN154-197442A:126-154
B:126-154
29
29
1.6ENSBTAT000000242336ENSBTAE00000197236chr5:108393940-108394066127MPRD_BOVIN197-239430--
1.7ENSBTAT000000242337ENSBTAE00000197238chr5:108394495-1083960421548MPRD_BOVIN240-279400--

(-) 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:151
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:151
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           MPRD_BOVIN    32 KTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3cy4a_ A: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                       SCOP domains
               CATH domains 3cy4A00 A:4-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:4-33         -------------------------------------------------------Exon 1.4  PDB: A:89-125              Exon 1.5  PDB: A:126-154      Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3  PDB: A:33-89 UniProt: 61-117                   ----------------------------------------------------------------- Transcript 1 (2)
                 3cy4 A   4 KTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:154
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178    
           MPRD_BOVIN    29 TEEKTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d3cy4b_ B: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                          SCOP domains
               CATH domains 3cy4B00 B:1-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:1-33            -------------------------------------------------------Exon 1.4  PDB: B:89-125              Exon 1.5  PDB: B:126-154      Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.3  PDB: B:33-89 UniProt: 61-117                   ----------------------------------------------------------------- Transcript 1 (2)
                 3cy4 B   1 TEEKTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CY4)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MPRD_BOVIN | P11456)
molecular function
    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:0015578    mannose transmembrane transporter activity    Enables the transfer of mannose from one side of the membrane to the other. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.
biological process
    GO:0015761    mannose transport    The directed movement of mannose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Mannose is the aldohexose manno-hexose, the C-2 epimer of glucose. The D-(+)-form is widely distributed in mannans and hemicelluloses and is of major importance in the core oligosaccharide of N-linked oligosaccharides of glycoproteins.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    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:0000323    lytic vacuole    A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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
        MPRD_BOVIN | P114561c39 1keo 1m6p 2rl7 2rl8 2rl9 2rlb 3k41 3k42 3k43

(-) Related Entries Specified in the PDB File

2rl7 2rl8 2rl9 2rlb