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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT SOYBEAN PROGLYCININ A3B4 SUBUNIT, ITS COMPARISON WITH MATURE GLYCININ A3B4 SUBUNIT, RESPONSIBLE FOR HEXAMER ASSEMBLY
 
Authors :  T. Itoh, M. Adachi, T. Masuda, B. Mikami, S. Utsumi
Date :  01 Nov 05  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Glycinin, Soybean, Globulin, 11S, Seed Storage Protein, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Tandang-Silvas, T. Fukuda, C. Fukuda, K. Prak, C. Cabanos, A. Kimura, T. Itoh, B. Mikami, S. Utsumi, N. Maruyama
Conservation And Divergence On Plant Seed 11S Globulins Based On Crystal Structures.
Biochim. Biophys. Acta 2010
PubMed-ID: 20215054  |  Reference-DOI: 10.1016/J.BBAPAP.2010.02.016

(-) Compounds

Molecule 1 - GLYCININ A3B4 SUBUNIT
    Chains: A, B
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Tissue: SEED

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CO32Ligand/IonCARBONATE ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CO36Ligand/IonCARBONATE ION
2CSD6Mod. Amino Acid3-SULFINOALANINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:50 , HIS A:58 , TYR A:131 , THR A:133BINDING SITE FOR RESIDUE CO3 A 501
2AC2SOFTWAREARG B:50 , HIS B:58 , TYR B:131 , THR B:133BINDING SITE FOR RESIDUE CO3 B 502
3AC3SOFTWAREHIS B:383 , GLU B:432 , TYR B:441BINDING SITE FOR RESIDUE MG B 601
4AC4SOFTWAREHIS A:383 , GLU A:432 , TYR A:441 , HOH A:1275BINDING SITE FOR RESIDUE MG A 602

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:9 -A:42
2A:85 -A:327
3B:9 -B:42
4B:85 -B:327

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D5F)

(-) Exons   (0, 0)

(no "Exon" information available for 2D5F)

(-) 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:384
 aligned with Q7GC77_SOYBN | Q7GC77 from UniProtKB/TrEMBL  Length:517

    Alignment length:487
                                    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       420       430       440       450       460       470       480       490       500       510       
         Q7GC77_SOYBN    31 NECQLNNLNALEPDHRVESEGGLIETWNSQHPELQCAGVTVSKRTLNRNGLHLPSYSPYPQMIIVVQGKGAIGFAFPGCPETFEKPQQQSSRRGSRSQQQLQDSHQKIRHFNEGDVLVIPPGVPYWTYNTGDEPVVAISLLDTSNFNNQLDQNPRVFYLAGNPDIEHPETMQQQQQQKSHGGRKQGQHQQQEEEGGSVLSGFSKHFLAQSFNTNEDTAEKLRSPDDERKQIVTVEGGLSVISPKWQEQEDEDEDEDEEYEQTPSYPPRRPSHGKHEDDEDEDEEEDQPRPDHPPQRPSRPEQQEPRGRGCQTRNGVEENICTMKLHENIARPSRADFYNPKAGRISTLNSLTLPALRQFGLSAQYVVLYRNGIYSPHWNLNANSVIYVTRGKGRVRVVNCQGNAVFDGELRRGQLLVVPQNFVVAEQGGEQGLEYVVFKTHHNAVSSYIKDVFRAIPSEVLSNSYNLGQSQVRQLKYQGNSGPLVNP 517
               SCOP domains d2d5fa1 A:7-249 automated matches                                                                                                                                                                                                                  --                                                                     -----d2d5fa2 A:326-493 automated matches                                                                                                                                      SCOP domains
               CATH domains 2d5fA01 A:7-335 Jelly Rolls                                                                                                                                                                                                                                                                                                              2d5fA02 A:336-493 Jelly Rolls                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...eeeee....hhhhhhhh.eeeeeee...eeeeeee....eeeeeee.eeeeee........eee.-------------...eee..eeeee..eeeee.....eeeee.....eeeeeee...............ee........hhhhh.---------------------...hhhhhhhhhhhhhhh..hhhhhhhh.........eee............---------------------------------------------------------------------....hhhhh..eee..hhhhh.eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeeeeeeeeeee.....eeeeeeee...eeee....eeeeeeeeeeeeeeeee......eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5f A   7 NECQLNNLNALEPDHRVESEGGLIETWNSQHPELQCAGVTVSKRTLNRNGLHLPSYSPYPQMIIVVQGKGAIGFAFPGCPETFEKP-------------QLQDSHQKIRHFNEGDVLVIPPGVPYWTYNTGDEPVVAISLLDTSNFNNQLDQNPRVFYLAGNPDIEHPETMQ---------------------EGGSVLSGFSKHFLAQSFNTNEDTAEKLRSPDDERKQIVTVEGGLSVISPKW---------------------------------------------------------------------GVEENICTMKLHENIARPSRADFYNPKAGRISTLNSLTLPALRQFGLSAQYVVLYRNGIYSPHWNLNANSVIYVTRGKGRVRVVNcQGNAVFDGELRRGQLLVVPQNFVVAEQGGEQGLEYVVFKTHHNAVSSYIKDVFRAIPSEVLSNSYNLGQSQVRQLKYQGNSGPLVNP 493
                                    16        26        36        46        56        66        76        86     |   -       106       116       126       136       146       156       166       176 |       -         -   |   206       216       226       236       246    |    -         -         -         -         -         -         -    |  326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       
                                                                                                                92           106                                                                     178                   200                                                251                                                                   321                                                                                  406-CSD                                                                                   


Chain B from PDB  Type:PROTEIN  Length:385
 aligned with Q7GC77_SOYBN | Q7GC77 from UniProtKB/TrEMBL  Length:517

    Alignment length:487
                                    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       420       430       440       450       460       470       480       490       500       510       
         Q7GC77_SOYBN    31 NECQLNNLNALEPDHRVESEGGLIETWNSQHPELQCAGVTVSKRTLNRNGLHLPSYSPYPQMIIVVQGKGAIGFAFPGCPETFEKPQQQSSRRGSRSQQQLQDSHQKIRHFNEGDVLVIPPGVPYWTYNTGDEPVVAISLLDTSNFNNQLDQNPRVFYLAGNPDIEHPETMQQQQQQKSHGGRKQGQHQQQEEEGGSVLSGFSKHFLAQSFNTNEDTAEKLRSPDDERKQIVTVEGGLSVISPKWQEQEDEDEDEDEEYEQTPSYPPRRPSHGKHEDDEDEDEEEDQPRPDHPPQRPSRPEQQEPRGRGCQTRNGVEENICTMKLHENIARPSRADFYNPKAGRISTLNSLTLPALRQFGLSAQYVVLYRNGIYSPHWNLNANSVIYVTRGKGRVRVVNCQGNAVFDGELRRGQLLVVPQNFVVAEQGGEQGLEYVVFKTHHNAVSSYIKDVFRAIPSEVLSNSYNLGQSQVRQLKYQGNSGPLVNP 517
               SCOP domains d2d5fb1 B:7-249 automated matches                                                                                                                                                                                                                  --                                                                     -----d2d5fb2 B:326-493 automated matches                                                                                                                                      SCOP domains
               CATH domains 2d5fB01 B:7-335 Jelly Rolls                                                                                                                                                                                                                                                                                                              2d5fB02 B:336-493 Jelly Rolls                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee...eeeee....hhhhhhhh.eeeeeee...eeeeeee....eeeeeee.eeeeee........eee..------------...eee..eeeee..eeeee.....eeeee.....eeeeeee...............ee........hhhhhh---------------------....hhhhhhhhhhhhhh..hhhhhhhh.........eee............---------------------------------------------------------------------....hhhhh..eee..hhhhh.eee...eeeeee......hhhhhh.eeeeeee....eeeeeee....eeeeeeeeeeeeeee.....eeeeeeee...eeee....eeeeeeeeeeeeeeeee......eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5f B   7 NECQLNNLNALEPDHRVESEGGLIETWNSQHPELQCAGVTVSKRTLNRNGLHLPSYSPYPQMIIVVQGKGAIGFAFPGCPETFEKPQ------------QLQDSHQKIRHFNEGDVLVIPPGVPYWTYNTGDEPVVAISLLDTSNFNNQLDQNPRVFYLAGNPDIEHPETMQ---------------------EGGSVLSGFSKHFLAQSFNTNEDTAEKLRSPDDERKQIVTVEGGLSVISPKW---------------------------------------------------------------------GVEENICTMKLHENIARPSRADFYNPKAGRISTLNSLTLPALRQFGLSAQYVVLYRNGIYSPHWNLNANSVIYVTRGKGRVRVVNcQGNAVFDGELRRGQLLVVPQNFVVAEQGGEQGLEYVVFKTHHNAVSSYIKDVFRAIPSEVLSNSYNLGQSQVRQLKYQGNSGPLVNP 493
                                    16        26        36        46        56        66        76        86      |  -       106       116       126       136       146       156       166       176 |       -         -   |   206       216       226       236       246    |    -         -         -         -         -         -         -    |  326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       
                                                                                                                 93          106                                                                     178                   200                                                251                                                                   321                                                                                  406-CSD
   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  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D5F)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7GC77_SOYBN | Q7GC77)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7GC77_SOYBN | Q7GC77: 1od5 2d5h

(-) Related Entries Specified in the PDB File

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