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(-) Description

Title :  COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN
 
Authors :  G. Prag, S. Lee, R. Mattera, C. N. Arighi, B. M. Beach, J. S. Bonifacino, J. H. Hurley
Date :  23 Dec 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  G,H,U,V
Biol. Unit 1:  H,U  (1x)
Biol. Unit 2:  G,V  (1x)
Keywords :  Trafficking, Post Translational Modification, Mono- Ubiquitination, Protein Transport; , Protein Transport, Chromosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Prag, S. Lee, R. Mattera, C. N. Arighi, B. M. Beach, J. S. Bonifacino, J. H. Hurley
Structural Mechanism For Ubiquitinated-Cargo Recognition By The Golgi-Localized, {Gamma}-Ear-Containing, Adp-Ribosylation-Factor-Binding Proteins
Proc. Natl. Acad. Sci. Usa V. 102 2334 2005
PubMed-ID: 15701688  |  Reference-DOI: 10.1073/PNAS.0500118102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUIN
    ChainsU, V
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    TissueRED BLOOD CELLS
 
Molecule 2 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
    ChainsG, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-PARALLEL.3_HIS6_GAT
    Expression System StrainBL21(DE3) ROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGGA3, KIAA0154
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF- BINDING PROTEIN 3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit GHUV
Biological Unit 1 (1x) HU 
Biological Unit 2 (1x)G  V

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YD8)

(-) Sites  (0, 0)

(no "Site" information available for 1YD8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YD8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YD8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YD8)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
  2U:1-73
V:1-73
RL40_BOVIN1-76
 
  2U:1-73
V:1-73
UBB_BOVIN1-76
77-152
153-228
229-304
 
  2-
-
-
U:1-73
V:1-73
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
  2-
-
-
-
-
-
-
-
U:1-73
V:1-73
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
  2U:27-52
V:27-52
RL40_BOVIN27-52
 
  2U:27-52
V:27-52
UBB_BOVIN27-52
103-128
179-204
255-280
 
  2-
-
-
U:27-52
V:27-52
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
  2-
-
-
-
-
-
-
-
U:27-52
V:27-52
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
  1U:1-73
-
RL40_BOVIN1-76
 
  1U:1-73
-
UBB_BOVIN1-76
77-152
153-228
229-304
 
  1-
-
-
U:1-73
-
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
  1-
-
-
-
-
-
-
-
U:1-73
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
  1U:27-52
-
RL40_BOVIN27-52
 
  1U:27-52
-
UBB_BOVIN27-52
103-128
179-204
255-280
 
  1-
-
-
U:27-52
-
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
  1-
-
-
-
-
-
-
-
U:27-52
-
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
  1-
V:1-73
RL40_BOVIN1-76
 
  1-
V:1-73
UBB_BOVIN1-76
77-152
153-228
229-304
 
  1-
-
-
-
V:1-73
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
  1-
-
-
-
-
-
-
-
-
V:1-73
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
  1-
V:27-52
RL40_BOVIN27-52
 
  1-
V:27-52
UBB_BOVIN27-52
103-128
179-204
255-280
 
  1-
-
-
-
V:27-52
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
  1-
-
-
-
-
-
-
-
-
V:27-52

(-) Exons   (0, 0)

(no "Exon" information available for 1YD8)

(-) 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 G from PDB  Type:PROTEIN  Length:93
 aligned with GGA3_HUMAN | Q9NZ52 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:93
                                   216       226       236       246       256       266       276       286       296   
           GGA3_HUMAN   207 RIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG 299
               SCOP domains -d1yd8g1 G:208-299 ADP-ribosylation factor binding protein Gga3                               SCOP domains
               CATH domains 1yd8G00 G:-1-299  [code=1.20.58.160, no name defined]                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1yd8 G  -1 GIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG 299
                            ||     216       226       236       246       256       266       276       286       296   
                            ||                                                                                           
                           -1|                                                                                           
                           208                                                                                           

Chain H from PDB  Type:PROTEIN  Length:93
 aligned with GGA3_HUMAN | Q9NZ52 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:93
                                   216       226       236       246       256       266       276       286       296   
           GGA3_HUMAN   207 RIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG 299
               SCOP domains d1yd8h_ H: ADP-ribosylation factor binding protein Gga3                                       SCOP domains
               CATH domains 1yd8H00 H:-1-299  [code=1.20.58.160, no name defined]                                         CATH domains
           Pfam domains (1) -GAT-1yd8H01 H:208-299                                                                        Pfam domains (1)
           Pfam domains (2) -GAT-1yd8H02 H:208-299                                                                        Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1yd8 H  -1 GIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG 299
                            ||     216       226       236       246       256       266       276       286       296   
                           -1|                                                                                           
                           208                                                                                           

Chain U from PDB  Type:PROTEIN  Length:73
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:73
                                    10        20        30        40        50        60        70   
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d1yd8u_ U: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8U00 U:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: U:1-73 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------UBIQUITIN_1  PDB: U:27-52 --------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 U   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain U from PDB  Type:PROTEIN  Length:73
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    10        20        30        40        50        60        70   
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d1yd8u_ U: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8U00 U:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) UBIQUITIN_2  PDB: U:1-73 UniProt: 1-76                                    PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------UBIQUITIN_1  PDB: U:27-52 --------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 U   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain U from PDB  Type:PROTEIN  Length:73
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:73
                                   238       248       258       268       278       288       298   
            UBB_BOVIN   229 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301
               SCOP domains d1yd8u_ U: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8U00 U:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: U:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: U:1-73 UniProt: 229-304                                 PROSITE (1)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 U   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain U from PDB  Type:PROTEIN  Length:73
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:73
                                   618       628       638       648       658       668       678   
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 681
               SCOP domains d1yd8u_ U: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8U00 U:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: U:1-73 UniProt: 609-684                                 PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: U:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ------------------------------------------------------------------------- PROSITE (7)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 U   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain V from PDB  Type:PROTEIN  Length:73
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:73
                                    10        20        30        40        50        60        70   
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d1yd8v_ V: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8V00 V:1-73                                                            CATH domains
           Pfam domains (1) -----ubiquitin-1yd8V01 V:6-73                                             Pfam domains (1)
           Pfam domains (2) -----ubiquitin-1yd8V02 V:6-73                                             Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: V:1-73 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------UBIQUITIN_1  PDB: V:27-52 --------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 V   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain V from PDB  Type:PROTEIN  Length:73
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    10        20        30        40        50        60        70   
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d1yd8v_ V: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8V00 V:1-73                                                            CATH domains
           Pfam domains (1) -----ubiquitin-1yd8V01 V:6-73                                             Pfam domains (1)
           Pfam domains (2) -----ubiquitin-1yd8V02 V:6-73                                             Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) UBIQUITIN_2  PDB: V:1-73 UniProt: 1-76                                    PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------UBIQUITIN_1  PDB: V:27-52 --------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 V   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain V from PDB  Type:PROTEIN  Length:73
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:73
                                   238       248       258       268       278       288       298   
            UBB_BOVIN   229 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301
               SCOP domains d1yd8v_ V: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8V00 V:1-73                                                            CATH domains
           Pfam domains (1) -----ubiquitin-1yd8V01 V:6-73                                             Pfam domains (1)
           Pfam domains (2) -----ubiquitin-1yd8V02 V:6-73                                             Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: V:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: V:1-73 UniProt: 229-304                                 PROSITE (1)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 V   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain V from PDB  Type:PROTEIN  Length:73
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:73
                                   618       628       638       648       658       668       678   
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 681
               SCOP domains d1yd8v_ V: Ubiquitin                                                      SCOP domains
               CATH domains 1yd8V00 V:1-73                                                            CATH domains
           Pfam domains (1) -----ubiquitin-1yd8V01 V:6-73                                             Pfam domains (1)
           Pfam domains (2) -----ubiquitin-1yd8V02 V:6-73                                             Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: V:1-73 UniProt: 609-684                                 PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: V:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ------------------------------------------------------------------------- PROSITE (7)
                 Transcript ------------------------------------------------------------------------- Transcript
                 1yd8 V   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)
(-)
Family: GAT (6)
2aGAT-1yd8H01H:208-299
2bGAT-1yd8H02H:208-299

(-) Gene Ontology  (23, 36)

Asymmetric Unit(hide GO term definitions)
Chain G,H   (GGA3_HUMAN | Q9NZ52)
molecular function
    GO:0030306    ADP-ribosylation factor binding    Interacting selectively and non-covalently with ARF, ADP-ribosylation factor, a small monomeric cytosolic GTPase that, when bound to GTP, binds to the membranes of cells.
    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).
biological process
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    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:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

Chain U,V   (UBB_BOVIN | P0CG53)
molecular function
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain U,V   (UBC_BOVIN | P0CH28)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain U,V   (RL40_BOVIN | P63048)
molecular function
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain U,V   (RS27A_BOVIN | P62992)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGA3_HUMAN | Q9NZ521jpl 1juq 1lf8 1p4u 1wr6
        RL40_BOVIN | P630481aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4ljo 4ljp 4s22
        RS27A_BOVIN | P629921aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4m0w 4y1h 4z9s 5bz0 5fer 5jqs 5mn9
        UBB_BOVIN | P0CG531aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 3h1u 3m3j 4bbn
        UBC_BOVIN | P0CH281aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 2zcc 3h1u 3m3j 4bbn 4xkh 4xyz 5ait

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YD8)