Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE
 
Authors :  L. J. Olson, J. Zhang, Y. C. Lee, N. M. Dahms, J. J. -P. Kim
Date :  25 Jul 99  (Deposition) - 14 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor, Cation Dependent Mannose 6-Phosphate, P-Type Lect Transport, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Olson, J. Zhang, Y. C. Lee, N. M. Dahms, J. J. Kim
Structural Basis For Recognition Of Phosphorylated High Mannose Oligosaccharides By The Cation-Dependent Mannose 6-Phosphate Receptor.
J. Biol. Chem. V. 274 29889 1999
PubMed-ID: 10514470  |  Reference-DOI: 10.1074/JBC.274.42.29889
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Atcc Number: 5B1-4
    Expression System Cell Line: 5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector: BACULOVIRUS
    Fragment: EXTRACYTOPLASMIC DOMAIN
    Mutation: YES
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: CDMPR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3P3M2Ligand/Ion1-3 SUGAR RING OF PENTAMANNOSYL 6-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:60 , ASN A:81 , GLU A:82 , NAG A:202BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWARENAG A:201BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWAREASN B:81 , GLU B:82 , NAG B:202 , HOH B:656BINDING SITE FOR RESIDUE NAG B 201
4AC4SOFTWAREARG B:79 , NAG B:201BINDING SITE FOR RESIDUE NAG B 202
5AC5SOFTWAREASP A:103 , ARG A:111 , P3M A:1200BINDING SITE FOR RESIDUE MN A 199
6AC6SOFTWAREASP B:103 , HOH B:649 , HOH B:650 , HOH B:659 , HOH B:671 , P3M B:2200BINDING SITE FOR RESIDUE MN B 199
7AC7SOFTWARELYS A:12 , PRO A:42 , ASP A:43 , TYR A:45 , GLN A:66 , GLN A:68 , TYR A:102 , ASP A:103 , ASN A:104 , HIS A:105 , ARG A:111 , GLU A:133 , ARG A:135 , TYR A:143 , MN A:199BINDING SITE FOR RESIDUE P3M A 1200
8AC8SOFTWAREASP B:43 , TYR B:45 , GLN B:66 , GLN B:68 , TYR B:102 , ASP B:103 , ASN B:104 , HIS B:105 , ARG B:111 , GLU B:133 , ARG B:135 , TYR B:143 , MN B:199 , HOH B:649 , HOH B:650BINDING SITE FOR RESIDUE P3M B 2200

(-) 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 1C39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C39)

(-) 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:3-33
B:3-33		31
31
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:152
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:152
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           MPRD_BOVIN    31 EKTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d1c39a_ A: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                        SCOP domains
               CATH domains 1c39A00 A:3-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee....eeeeeeeeeeeeeee...eeeeeeee......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:3-33          -------------------------------------------------------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)
                 1c39 A   3 EKTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with MPRD_BOVIN | P11456 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:152
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
           MPRD_BOVIN    31 EKTCDLVGEKGKESEKELALLKRLTPLFNKSFESTVGQSPDMYSYVFRVCREAGNHSSGAGLVQINKSNGKETVVGRFNETQIFNGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 182
               SCOP domains d1c39b_ B: Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain                                                                        SCOP domains
               CATH domains 1c39B00 B:3-154 Cation-dependent Mannose-6-phosphate Receptor; Chain A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeee......eeeee............eeeeeee.....eeeeeeeeeeeeee...eeeeeee.......hhhhh...eeeeeee......eeeeeeeee.......eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:3-33          -------------------------------------------------------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)
                 1c39 B   3 EKTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C39)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P3M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:41 - Pro A:42   [ RasMol ]  
    Ser B:41 - Pro B:42   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1c39
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MPRD_BOVIN | P11456
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MPRD_BOVIN | P11456
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MPRD_BOVIN | P11456: 1keo 1m6p 2rl7 2rl8 2rl9 2rlb 3cy4 3k41 3k42 3k43

(-) Related Entries Specified in the PDB File

1m6p STRUCRURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO MANNOSE 6-PHOSPHATE