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(-) Description

Title :  STRUCTURE OF NEDD8
 
Authors :  F. G. Whitby, G. Xia, C. M. Pickart, C. P. Hill
Date :  21 Aug 98  (Deposition) - 23 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Nedd8, Nedd-8, Ubiquitin-Like, Proteolysis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. G. Whitby, G. Xia, C. M. Pickart, C. P. Hill
Crystal Structure Of The Human Ubiquitin-Like Protein Nedd8 And Interactions With Ubiquitin Pathway Enzymes.
J. Biol. Chem. V. 273 34983 1998
PubMed-ID: 9857030  |  Reference-DOI: 10.1074/JBC.273.52.34983

(-) Compounds

Molecule 1 - PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A-NEDD8
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsHUMAN NEDD8 UBIQUITIN-LIKE PROTEIN MONOMER WITH 4 MOLECULES IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
    Other Details - SourceEXPRESSED IN E.COLI
    SynonymNEDD8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO43Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:171 , HOH B:1036 , LEU C:271BINDING SITE FOR RESIDUE CL B 2001
2AC2SOFTWARELEU A:71 , HOH A:1054 , LEU D:371 , HOH D:1068BINDING SITE FOR RESIDUE CL A 2002
3AC3SOFTWARELYS D:327 , GLN D:341 , ARG D:342 , GLN D:349 , HOH D:1043BINDING SITE FOR RESIDUE SO4 D 3001
4AC4SOFTWARESER A:46 , ASN C:251 , LYS C:254 , HOH C:1088BINDING SITE FOR RESIDUE SO4 C 3002
5AC5SOFTWARELYS C:227 , ARG C:242 , HOH C:1008 , HOH C:1038BINDING SITE FOR RESIDUE SO4 C 3003
6AC6SOFTWARELYS A:48 , GLN A:49 , LYS C:248 , LYS C:260BINDING SITE FOR RESIDUE SO4 C 3004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  4A:1-74
B:101-176
C:201-273
D:301-373
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  4A:27-52
B:127-152
C:227-252
D:327-352
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  1A:1-74
-
-
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  1A:27-52
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  1-
B:101-176
-
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  1-
B:127-152
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  1-
-
C:201-273
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  1-
-
C:227-252
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  1-
-
-
D:301-373
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  1-
-
-
D:327-352
Biological Unit 5 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
 
 
  4A:1-74
B:101-176
C:201-273
D:301-373
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
 
 
  4A:27-52
B:127-152
C:227-252
D:327-352

(-) Exons   (4, 16)

Asymmetric Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-664A:1-6
B:101-106
C:201-206
D:301-306
6
6
6
6
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22164A:7-22
B:107-122
C:207-222
D:307-322
16
16
16
16
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50284A:23-50
B:123-150
C:223-250
D:323-350
28
28
28
28
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81324A:50-74
B:150-176
C:250-273
D:350-373
25
27
24
24

(-) 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:74
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:74
                                    10        20        30        40        50        60        70    
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR  74
               SCOP domains d1ndda_ A: Nedd8                                                           SCOP domains
               CATH domains 1nddA00 A:1-74                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee......hhhhhhhhhhhh...hhheeee...........hhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-74 UniProt: 1-76                                     PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: A:27-52 ---------------------- PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: A:23-50     ------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: A:50-74   Transcript 1 (2)
                 1ndd A   1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR  74
                                    10        20        30        40        50        60        70    

Chain B from PDB  Type:PROTEIN  Length:76
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
               SCOP domains d1nddb_ B: Nedd8                                                             SCOP domains
               CATH domains 1nddB00 B:101-176                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee......hhhhhhhhhhhh...hhheeee.....................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: B:101-176 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: B:127-15------------------------ PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: B:123-150   -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: B:150-176   Transcript 1 (2)
                 1ndd B 101 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 176
                                   110       120       130       140       150       160       170      

Chain C from PDB  Type:PROTEIN  Length:73
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:73
                                    10        20        30        40        50        60        70   
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL  73
               SCOP domains d1nddc_ C: Nedd8                                                          SCOP domains
               CATH domains 1nddC00 C:201-273                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee......hhhhhhhhhhhh...hhheeee............hhh......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: C:201-273 UniProt: 1-76                                 PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: C:227-25--------------------- PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: C:223-250   ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: C:250-27 Transcript 1 (2)
                 1ndd C 201 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL 273
                                   210       220       230       240       250       260       270   

Chain D from PDB  Type:PROTEIN  Length:73
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:73
                                    10        20        30        40        50        60        70   
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL  73
               SCOP domains d1nddd_ D: Nedd8                                                          SCOP domains
               CATH domains 1nddD00 D:301-373                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee......hhhhhhhhhhhh...hhheeee.....................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: D:301-373 UniProt: 1-76                                 PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: D:327-35--------------------- PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: D:323-350   ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: D:350-37 Transcript 1 (2)
                 1ndd D 301 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL 373
                                   310       320       330       340       350       360       370   

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NEDD8_HUMAN | Q15843)
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).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEDD8_HUMAN | Q158431r4m 1r4n 1xt9 2bkr 2ko3 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o

(-) Related Entries Specified in the PDB File

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