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(-) Description

Title :  CRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYCININ BETA HOMOTRIMERS COMPLEXES WITH N-ACETYL-D-GLUCOSAMINE
 
Authors :  N. Maruyama, M. Adachi, K. Takahashi, K. Yagasaki, M. Kohno, Y. Takenak E. Okuda, S. Nakagawa, B. Mikami, S. Utsumi
Date :  16 May 01  (Deposition) - 16 May 02  (Release) - 13 Jul 11  (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

(-) Compounds

Molecule 1 - BETA-CONGLYCININ, BETA CHAIN
    Chains: A, B, C
    Organ: SEED
    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  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:283 , ASN A:329 , THR A:331 , ALA A:393 , ASN C:157 , ILE C:158 , THR C:161BINDING SITE FOR RESIDUE NAG A 902
2AC2SOFTWAREASN A:157 , ILE A:158 , GLY B:260 , ARG B:309 , ASN B:329 , ALA B:393BINDING SITE FOR RESIDUE NAG B 903
3AC3SOFTWARETHR B:161 , LEU C:262 , ASN C:329 , ALA C:393BINDING SITE FOR RESIDUE NAG C 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IPJ)

(-) 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:357
 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 d1ipja1 A:9-176 Seed storage 7S protein                                                                                                                                       d1ipja2 A:          183-393 Seed storage 7S protein                                                                                                                                                                 SCOP domains
               CATH domains 1ipjA02 A:9-204 Jelly Rolls                                                                                                                                                                         ----------1ipjA01 A:215-390 Jelly Rolls                                                                                                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhh.eeeeee...eeeeee.hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeeee......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhhhh..------.....eee..----------.ee............ee.......eee..eeeeee....hhhhhhhh.eeeeeee...eeeeeeee...eeeeeeee..eeeeeeee.------------..eeeeeeee....eeee.....eeee....eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipj A   9 NNPFYLRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLLG------QQEGVIVELS----------AKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIK------------LEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 393
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       | -    |  188   |     -    |  208       218       228       238       248       258       268       278       288 |       -    |  308       318       328       338       348       358       368       378       388     
                                                                                                                                                                                                 176    183      192        203                                                                                    290          303                                                                                          


Chain B from PDB  Type:PROTEIN  Length:363
 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 d1ipjb1 B:9-175 Seed storage 7S protein                                                                                                                                          d1ipjb2 B:186-393 Seed storage 7S protein                                                                                                                                                                        SCOP domains
               CATH domains 1ipjB02 B:9-194 Jelly Rolls                                                                                                                                                               --------------------1ipjB01 B:215-391 Jelly Rolls                                                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhh..eeeee..eeeee..hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeee.......eeeeeeeee........eee........hhhhh.hhhhhhhhh..hhhhhhhhh.----------..eee.hhhhhhhhhh.....hhhhh......ee.......eee..eeeeee....hhhhhh..eeeeeeee....eeeeeee...eeeeeeee..eeeeeeee.------------..eeeeeeee....eeee.....eeeee...eeeeeeee......eee.......hhhh.hhhhhhhhh..hhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipj B   9 NNPFYLRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLL----------GVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIK------------LEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 393
                                    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     
                                                                                                                                                                                                175        186                                                                                                     290          303                                                                                          


Chain C 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 d1ipjc1 C:9-177 Seed storage 7S protein                                                                                                                                     d1ipjc2 C:181-393 Seed storage 7S protein                                                                                                                                                                             SCOP domains
               CATH domains 1ipjC02 C:9-194 Jelly Rolls                                                                                                                                                               --------------------1ipjC01 C:215-391 Jelly Rolls                                                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhh.eeeeeee..eeeeee.hhhhhhhhhhhhh..eeeeeee...eeeeeeee.eeeeeeeee..eeeeee....eeeeee...eeeee....eeeee.......eeeeeeeee........eee........hhhhhhhhhhhhhhhh.hhhhhhh.....---.......eee.hhhhhhhhh...ee.hhhhh......ee.......eee..eee.......hhhhhhh.eeeeeeee...eeeeeeee...eeeeeeee..eeeee...--------------......eee....eeee.....eeeee...eeeeeeee......eee.......hhhh.hhhhhhhhh..hhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipj C   9 NNPFYLRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLLGE---QRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGI--------------EVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDA 393
                                    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     
                                                                                                                                                                                                  177 181                                                                                                         289            304
   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)
1a1ipjC01C:215-391
1b1ipjA01A:215-390
1c1ipjB01B:215-391
1d1ipjB02B:9-194
1e1ipjA02A:9-204
1f1ipjC02C:9-194

(-) Pfam Domains  (0, 0)

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

(-) 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: 1ipk 1uij

(-) Related Entries Specified in the PDB File

1ipk 1IPK CONTAINS THE SAME PROTEIN