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(-) Description

Title :  CRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYCININ BETA HOMOTRIMERS
 
Authors :  N. Maruyama, M. Adachi, K. Takahashi, K. Yagasaki, M. Kohno, Y. Takenaka, E. Okuda, S. Nakagawa, B. Mikami, S. Utsumi
Date :  16 May 01  (Deposition) - 16 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Soybean, Storage Protein, Vicilin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maruyama, M. Adachi, K. Takahashi, K. Yagasaki, M. Kohno, Y. Takenaka, E. Okuda, S. Nakagawa, B. Mikami, S. Utsumi
Crystal Structures Of Recombinant And Native Soybean Beta-Conglycinin Beta Homotrimers.
Eur. J. Biochem. V. 268 3595 2001
PubMed-ID: 11422391  |  Reference-DOI: 10.1046/J.1432-1327.2001.02268.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-CONGLYCININ, BETA CHAIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IPK)

(-) Sites  (0, 0)

(no "Site" information available for 1IPK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IPK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IPK)

(-) 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:368
 aligned with GLCB_SOYBN | P25974 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:385
                                    40        50        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     
           GLCB_SOYBN    31 NNPFYFRSSNSFQTLFENQNVRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQQQKQKQEEEPLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 415
               SCOP domains d1ipka1 A:8-174 Seed storage 7S protein                                                                                                                                        d1ipka2 A:183-392 Seed storage 7S protein                                                                                                                                                                          SCOP domains
               CATH domains 1ipkA02 A:8-193 Jelly Rolls                                                                                                                                                               --------------------1ipkA01 A:214-390 Jelly Rolls                                                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhheeeeee...eeeeee.hhhhhh.........eeeeeee...eee..eee.eeeeeeeee..eeeeeee..eeeeeee...eeeee....eeeeee......eeeeeeeee........eee..............hhhhhhhhhh....hhhhhh.--------....eee.hhhhhhhh....ee...hhhhh....ee.hhh...eee..eeeeee....hhhhhh...eeeeeee...eeeeeeee...eeeeee...eeeeeeeee...---------...eeeeeeee....eeee.....eeeeeee.eeeeeeee......eee............hhhhhh.........hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipk A   8 NNPFYFRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLF--------QEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQ---------PLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 392
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167      |  -     | 187       197       207       217       227       237       247       257       267       277       287   |     -   |   307       317       327       337       347       357       367       377       387     
                                                                                                                                                                                                174      183                                                                                                         291       301                                                                                           


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with GLCB_SOYBN | P25974 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:384
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
           GLCB_SOYBN    32 NPFYFRSSNSFQTLFENQNVRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQQQKQKQEEEPLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 415
               SCOP domains d1ipkb1 B:9-174 Seed storage 7S protein                                                                                                                                       d1ipkb2 B:183-392 Seed storage 7S protein                                                                                                                                                                          SCOP domains
               CATH domains 1ipkB02 B:9-193 Jelly Rolls                                                                                                                                                              --------------------1ipkB01 B:214-390 Jelly Rolls                                                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.......eeeee..eeeee..hhhhhhhhhhhhh..eeeeeee....ee..eee.eeeeeee....eeeeee....eeeeee...eeeee....eeeee.......eeeeeeeee........eee.........hhhhhhhhhhhhhhh.hhhhhhhhh.--------....ee..hhhhhhhh..................ee.......eee..eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeeeeeeeeeeeee..-----------..eeeeeeee....eeee.....eeeeeeeeeeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ipk B   9 NPFYFRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLF--------QEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKE-----------LEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 392
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     |   -    |  188       198       208       218       228       238       248       258       268       278       288 |       -   |   308       318       328       338       348       358       368       378       388    
                                                                                                                                                                                               174      183                                                                                                        290         302                                                                                          


Chain C from PDB  Type:PROTEIN  Length:379
 aligned with GLCB_SOYBN | P25974 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:390
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415
           GLCB_SOYBN    26 VREDENNPFYFRSSNSFQTLFENQNVRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQQQKQKQEEEPLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 415
               SCOP domains d1ipkc1 C:3-180 Seed storage 7S protein                                                                                                                                           d1ipkc2 C:181-392 Seed storage 7S protein                                                                                                                                                                            SCOP domains
               CATH domains -----1ipkC02 C:8-193 Jelly Rolls                                                                                                                                                               --------------------1ipkC01 C:214-391 Jelly Rolls                                                                                                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee.....eeeeeee..eeeeee.hhhhhhhhhhhhh..eeeeeee...eee..eee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeee.......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhh....eee.hhhhhhhhh...ee.hhhhh......ee.......eee..eeeeee....hhhhhh..eeeeeeee...eeeeeeee...eeeeeeee.eeeeeeeee.-----------...eeeeeeeee...eeee.....eeeee...eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ipk C   3 VREDENNPFYFRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIK-----------PLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 392
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      |  -       302       312       322       332       342       352       362       372       382       392
                                                                                                                                                                                                                                                                                                                        289         301
   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)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: Jelly Rolls (177)
(-)
Soybean (Glycine max) (10)
1a1ipkB01B:214-390
1b1ipkC01C:214-391
1c1ipkA01A:214-390
1d1ipkB02B:9-193
1e1ipkA02A:8-193
1f1ipkC02C:8-193

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (GLCB_SOYBN | P25974)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
cellular component
    GO:0033095    aleurone grain    A membrane-bounded storage granule found in cells of the aleurone layer in plants; contains either a protein matrix, protein-carbohydrate bodies and/or globoids. Aleurone grains are formed by the vacuole, rough endoplasmic reticulum and dictyosomes.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLCB_SOYBN | P25974: 1ipj 1uij

(-) Related Entries Specified in the PDB File

1ipj 1IPJ CONTAINS THE SAME PROTEIN COMPLEXED WITH N-ACETYL-D- GLUCOSAMINE