Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  NEDD8 NEDP1 COMPLEX
 
Authors :  L. N. Shen, H. Liu, C. Dong, D. Xirodimas, J. H. Naismith, R. T. Hay
Date :  18 Feb 05  (Deposition) - 15 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Binding-Hydrolase Complex, Ubiquitin, Hydrolase, Protease, Thiol Protease, Ubl Conjugation Pathway, Ubiquitin/Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. N. Shen, H. Liu, C. Dong, D. Xirodimas, J. H. Naismith, R. T. Hay
Structural Basis Of Nedd8 Ubiquitin Discrimination By The Deneddylating Enzyme Nedp1
Embo J. V. 24 1341 2005
PubMed-ID: 15775960  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600628

(-) Compounds

Molecule 1 - SENTRIN-SPECIFIC PROTEASE 8
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP8, CYSTEINE PROTEASE FKSG8, PROTEASE, CYSTEINE 2
 
Molecule 2 - NEDDYLIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDD8, UBIQUITIN-LIKE PROTEIN NEDD8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2BKR)

(-) Sites  (0, 0)

(no "Site" information available for 2BKR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BKR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:23 -Pro A:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023705T207ASENP8_HUMANPolymorphism930871AA207A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76  1B:1-76
2ULP_PROTEASEPS50600 Ubiquitin-like protease family profile.SENP8_HUMAN11-174  1A:11-174
3UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52  1B:27-52

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-661B:1-66
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22161B:7-2216
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50281B:23-5028
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81321B:50-7627

2.1ENST000003409121ENSE00001521305chr15:72410637-72410805169SENP8_HUMAN-00--
2.2ENST000003409122ENSE00001386768chr15:72431918-724333041387SENP8_HUMAN1-2282281A:1-212212

(-) 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:212
 aligned with SENP8_HUMAN | Q96LD8 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
          SENP8_HUMAN     1 MDPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDCSDHVSFISPEVTQFIKCTSNPAEIAMFLEPLDLPNKRVVFLAINDNSNQAAGGTHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNSYDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLITTLAKK 212
               SCOP domains d2bkra_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeehhhhhh.......hhhhhhhhhhhhhhh.hhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eeeeeee...........eeeeeee.hhheeeee......hhhhhhhhhhhhhhhhh.......eee..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----- SAPs(SNPs)
                PROSITE (2) ----------ULP_PROTEASE  PDB: A:11-174 UniProt: 11-174                                                                                                                         -------------------------------------- PROSITE (2)
               Transcript 2 Exon 2.2  PDB: A:1-212 UniProt: 1-228 [INCOMPLETE]                                                                                                                                                                   Transcript 2
                 2bkr A   1 MDPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDSSDHVSFISPEVTQFIKCTSNPAEIAMFLEPLDLPNKRVVFLAINDNSNQAAGGSHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNSYDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLIATLAKK 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:77
                             1                                                                           
                             |       9        19        29        39        49        59        69       
          NEDD8_HUMAN     - -MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
               SCOP domains d2bkrb_ B: automated matches                                                  SCOP domains
               CATH domains 2bkrB00 B:0-76                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -UBIQUITIN_2  PDB: B:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------UBIQUITIN_1  PDB: B:27-52 ------------------------ PROSITE (3)
           Transcript 1 (1) -1.1a  Exon 1.4        Exon 1.5a  PDB: B:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.6e  PDB: B:50-76     Transcript 1 (2)
                 2bkr B   0 SMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
                                     9        19        29        39        49        59        69       

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SENP8_HUMAN | Q96LD8)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2bkr)
 
  Sites
(no "Sites" information available for 2bkr)
 
  Cis Peptide Bonds
    Pro A:23 - Pro A:24   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bkr
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NEDD8_HUMAN | Q15843
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SENP8_HUMAN | Q96LD8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NEDD8_HUMAN | Q15843
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SENP8_HUMAN | Q96LD8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 1xt9 2ko3 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o
        SENP8_HUMAN | Q96LD81xt9 2bkq

(-) Related Entries Specified in the PDB File

1ndd STRUCTURE OF NEDD8
1r4m APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEX
1r4n APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEXWITH ATP
1xt9 CRYSTAL STRUCTURE OF DEN1 IN COMPLEX WITH NEDD8
2bkq NEDD8 PROTEASE