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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MONOBODY YSMB-1 BOUND TO YEAST SUMO
 
Authors :  S. Koide, R. N. Gilbreth
Date :  26 Jan 11  (Deposition) - 11 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Fibronectin Type Iii, Yeast Small Ubiquitin-Like Modifier, Smt3, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. N. Gilbreth, K. Truong, I. Madu, A. Koide, J. B. Wojcik, N. S. Li, J. A. Piccirilli, Y. Chen, S. Koide
Isoform-Specific Monobody Inhibitors Of Small Ubiquitin-Related Modifiers Engineered Using Structure-Guided Library Design.
Proc. Natl. Acad. Sci. Usa V. 108 7751 2011
PubMed-ID: 21518904  |  Reference-DOI: 10.1073/PNAS.1102294108

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN SMT3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSMT3, YDR510W, D9719.15
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymYEAST SMALL UBIQUITIN-LIKE MODIFIER (SUMO)
 
Molecule 2 - MONOBODY YSMB-1
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificARTIFICIAL GENE
    Organism Taxid32630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , HIS A:23 , ASN A:25 , LYS A:38 , ASP A:85 , GLU C:47BINDING SITE FOR RESIDUE GOL A 99
2AC2SOFTWARESER A:32 , SER A:33 , GLU A:34 , HOH A:107 , SER C:86BINDING SITE FOR RESIDUE GOL A 100
3AC3SOFTWARETYR A:67 , ASP A:68 , ASP A:87 , ILE A:88 , SER C:25 , HOH C:118BINDING SITE FOR RESIDUE GOL A 101
4AC4SOFTWAREASP A:68 , ILE A:70 , THR D:49BINDING SITE FOR RESIDUE GOL A 102
5AC5SOFTWAREASP A:75 , HOH A:116 , HOH A:117 , TYR D:78 , TYR D:79BINDING SITE FOR RESIDUE GOL A 103
6AC6SOFTWAREASP B:75 , GLY C:41 , TYR C:78 , TYR C:79 , HOH C:100BINDING SITE FOR RESIDUE GOL C 95
7AC7SOFTWAREHOH A:109 , PRO C:5 , THR C:6 , ASP C:23 , ALA C:24 , SER C:25 , SER C:26 , TYR C:32 , HOH C:116BINDING SITE FOR RESIDUE GOL C 96
8AC8SOFTWAREASN C:91 , TYR C:92 , ARG C:93BINDING SITE FOR RESIDUE GOL C 97

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QHT)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ile A:96 -Gly A:97
2Val C:4 -Pro C:5
3Ser D:3 -Val D:4
4Val D:4 -Pro D:5
5Ser D:27 -Ser D:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QHT)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SMT3_YEAST22-98
 
  2A:22-97
B:22-94
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SMT3_YEAST22-98
 
  1A:22-97
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SMT3_YEAST22-98
 
  1-
B:22-94

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR510W1YDR510W.1IV:1469393-1469698306SMT3_YEAST1-1011012A:19-97
B:22-94
79
73

(-) 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:79
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:79
                                    28        38        48        58        68        78        88         
            SMT3_YEAST   19 KPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG 97
               SCOP domains d3qhta_ A: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeee....hhhhhhhhhhhh..hhh.eeeee..ee...............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBIQUITIN_2  PDB: A:22-97 UniProt: 22-98                                     PROSITE
               Transcript 1 Exon 1.1  PDB: A:19-97 UniProt: 1-101 [INCOMPLETE]                              Transcript 1
                  3qht A 19 KPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG 97
                                    28        38        48        58        68        78        88         

Chain B from PDB  Type:PROTEIN  Length:73
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:73
                                    31        41        51        61        71        81        91   
            SMT3_YEAST   22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE 94
               SCOP domains d3qhtb_ B: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----ubiquitin-3qhtB01 B:27-94                                            Pfam domains (1)
           Pfam domains (2) -----ubiquitin-3qhtB02 B:27-94                                            Pfam domains (2)
         Sec.struct. author ..eeeeee....eeeeee.....hhhhhhhhhhh...hhhhheeee..ee...............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: B:22-94 UniProt: 22-98                                  PROSITE
               Transcript 1 Exon 1.1  PDB: B:22-94 UniProt: 1-101 [INCOMPLETE]                        Transcript 1
                  3qht B 22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE 94
                                    31        41        51        61        71        81        91   

Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains d3qhtc_ C: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeee.........eeeeeeee.......eeeeee....eeee.......eeeeeeeeeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3qht C  2 SSVPTKLEVVAATPTSLLISWDASSSSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYAYYSYYDLYYSYSPSSINYRT 94
                                    11        21        31        41        51        61        71        81        91   

Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains d3qhtd_ D: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeee.........eeeeeeee.......eeeeee....eeee.......eeeeeeeeeeee..eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3qht D  2 SSVPTKLEVVAATPTSLLISWDASSSSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYAYYSYYDLYYSYSPSSINYRT 94
                                    11        21        31        41        51        61        71        81        91   

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QHT)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SMT3_YEAST | Q12306)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005940    septin ring    A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SMT3_YEAST | Q123061euv 1l2n 2eke 3pge 3tix 3uf8 3uqa 3uqb 3v60 3v61 3v62 3vaw 4fn2 4g50 4ggq 4giv 5d6j 5jne 5klx

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