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(-) Description

Title :  CRYSTAL STRUCTURE OF EMP47P CARBOHYDRATE RECOGNITION DOMAIN (CRD), MONOCLINIC CRYSTAL FORM 2
 
Authors :  T. Satoh, K. Sato, A. Kanoh, K. Yamashita, R. Katoh, A. Nakano, S. Wakatsuki
Date :  04 Jul 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:148 , ALA A:149 , SER B:147 , ALA B:149 , SER B:150 , HOH B:266 , HOH B:450BINDING SITE FOR RESIDUE EDO B 1
2AC2SOFTWARESER A:150 , CYS A:151 , CYS A:185 , HOH A:260 , HOH A:509 , EDO B:3 , LEU B:123 , SER B:150BINDING SITE FOR RESIDUE EDO A 2
3AC3SOFTWAREEDO A:2 , LEU A:123 , SER A:150 , SER B:150 , CYS B:151 , CYS B:185 , HOH B:278 , HOH B:279 , HOH B:427BINDING SITE FOR RESIDUE EDO B 3
4AC4SOFTWARESER A:147 , ALA A:149 , SER A:150 , HOH A:243 , HOH A:442 , PHE B:148 , ALA B:149BINDING SITE FOR RESIDUE EDO A 4
5AC5SOFTWAREGLY A:112 , ASN A:132 , PRO A:194 , HOH A:286BINDING SITE FOR RESIDUE EDO A 5
6AC6SOFTWAREGLY B:112 , ASN B:132 , PHE B:193 , PRO B:194 , HOH B:292 , HOH B:330 , HOH B:462BINDING SITE FOR RESIDUE EDO B 228

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:151 -A:185
2B:151 -B:185

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A70)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LECTIN_LIKEPS51328 L-type lectin-like (leguminous) domain profile.EMP47_YEAST36-254
 		  2A:8-226
B:8-226
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LECTIN_LIKEPS51328 L-type lectin-like (leguminous) domain profile.EMP47_YEAST36-254
 		  1A:8-226
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LECTIN_LIKEPS51328 L-type lectin-like (leguminous) domain profile.EMP47_YEAST36-254
 		  1-
B:8-226

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFL048C1YFL048C.1VI:40180-388431338EMP47_YEAST1-4454452A:6-227
B:6-227		222
222

(-) 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:222
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:222
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
          EMP47_YEAST    34 TSDASKLSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a70a_ 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 --L_LECTIN_LIKE  PDB: A:8-226 UniProt: 36-254                                                                                                                                                                                - PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                             Transcript 1
                 2a70 A   6 GSDASKLSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with EMP47_YEAST | P43555 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:222
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
          EMP47_YEAST    34 TSDASKLSSDYSLPDLINARKVPNNWQTGEQASLEEGRIVLTSKQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNVPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 255
               SCOP domains d2a70b_ 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 --L_LECTIN_LIKE  PDB: B:8-226 UniProt: 36-254                                                                                                                                                                                - PROSITE
               Transcript 1 Exon 1.1  PDB: B:6-227 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                             Transcript 1
                 2a70 B   6 GSDASKLSSDYSLPDLINTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFTMEWTFRSVGYSGQTDGGISFWFVQDSNIPRDKQLYNGPVNYDGLQLLVDNNGPLGPTLRGQLNDGQKPVDKTKIYDQSFASCLMGYQDSSVPSTIRVTYDLEDDNLLKVQVDNKVCFQTRKVRFPSGSYRIGVTAQNGAVNNNAESFEIFKMQFFNGV 227
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A70)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  2a70
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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 2a71

(-) Related Entries Specified in the PDB File

1gv9 1r1z 2a6v 2a6w 2a6x 2a6y 2a6z 2a71