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(-) Description

Title :  CRYSTAL STRUCTURE OF EMP47P CARBOHYDRATE RECOGNITION DOMAIN (CRD), ORTHORHOMBIC CRYSTAL FORM
 
Authors :  T. Satoh, K. Sato, A. Kanoh, K. Yamashita, R. Kato, A. Nakano, S. Wakatsuki
Date :  04 Jul 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Sandwich, Carbohydrate Binding Protein, Cargo Receptor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, K. Sato, A. Kanoh, K. Yamashita, Y. Yamada, N. Igarashi, R. Kato, A. Nakano, S. Wakatsuki
Structures Of The Carbohydrate Recognition Domain Of Ca2+-Independent Cargo Receptors Emp46P And Emp47P.
J. Biol. Chem. V. 281 10410 2006
PubMed-ID: 16439369  |  Reference-DOI: 10.1074/JBC.M512258200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EMP47P
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 7-227
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2A71)

(-) Sites  (0, 0)

(no "Site" information available for 2A71)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:151 -A:185
2B:151 -B:185
3C:151 -C:185
4D:151 -D:185

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A71)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A71)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFL048C1YFL048C.1VI:40180-388431338EMP47_YEAST1-4454454A:11-227
B:9-227
C:11-227
D:12-227		217
219
217
216

(-) 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:217
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:217
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       
          EMP47_YEAST    39 KLSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a71a_ A: Emp47p N-terminal domain                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.............eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeee.......eeeeeeee.........hhhhh.eeee.........eeeeeeee.....eeeeee..eeeeee.........eeeeeeee.........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:11-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                       Transcript 1
                 2a71 A  11 KLSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:219
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
          EMP47_YEAST    37 ASKLSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a71b_ B: Emp47p N-terminal domain                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.............eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeee.......eeeeeeee.........hhhhh.eeee.........eeeeeeee.....eeeeee..eeeeee.........eeeeeeee.........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                          Transcript 1
                 2a71 B   9 ASKLSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:217
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       
          EMP47_YEAST    39 KLSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a71c_ C: Emp47p N-terminal domain                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.............eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeee.......eeeeeeee.........hhhhh.eeee.........eeeeeeee.....eeeeee..eeeeee.........eeeeeeee.........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:11-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                       Transcript 1
                 2a71 C  11 KLSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:216
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
          EMP47_YEAST    40 LSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a71d_ D: Emp47p N-terminal domain                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh.............eeeee..eee..eee.......eeeeee.........eeeeeeeeee........eeeeeeee.................eeeeeeee.......eeeeeeee.........hhhhh.eeee.........eeeeeeee.....eeeeee..eeeeee.........eeeeeeee.........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: D:12-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                      Transcript 1
                 2a71 D  12 LSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A71)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (EMP47_YEAST | P43555)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030173    integral component of Golgi membrane    The component of the Golgi 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:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum 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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  2a71
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  EMP47_YEAST | P43555
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 Related Entries

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

UniProtKB/Swiss-Prot
        EMP47_YEAST | P43555: 2a6y 2a6z 2a70

(-) Related Entries Specified in the PDB File

1gv9 1r1z 2a6v 2a6w 2a6x 2a6y 2a6z 2a70