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(-) Description

Title :  COMPLEX BETWEEN HUMAN RANGAP1-SUMO2, UBC9 AND THE IR1 DOMAIN FROM RANBP2 CONTAINING IR2 MOTIF II
 
Authors :  J. R. Gareau, D. Reverter, C. D. Lima
Date :  05 Nov 11  (Deposition) - 28 Dec 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  E3, Ligase, Sumo, Ubc9, Ranbp2, Nuclear Pore Complex, Ligase- Isomerase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Gareau, D. Reverter, C. D. Lima
Determinants Of Small Ubiquitin-Like Modifier 1 (Sumo1) Protein Specificity, E3 Ligase, And Sumo-Rangap1 Binding Activities Of Nucleoporin Ranbp2.
J. Biol. Chem. V. 287 4740 2012
PubMed-ID: 22194619  |  Reference-DOI: 10.1074/JBC.M111.321141

(-) Compounds

Molecule 1 - SUMO-CONJUGATING ENZYME UBC9
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBC9, UBCE9, UBE2I
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSUMO-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN 9, UBIQUITIN CARRIER PROTEIN I, UBIQUITIN-CONJUGATING ENZYME E2 I, UBIQUITIN- PROTEIN LIGASE I, P18
 
Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER 2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 14-93
    GeneSMT3A, SMT3H2, SUMO2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSUMO-2, HSMT3, SMT3 HOMOLOG 2, SUMO-3, SENTRIN-2, UBIQUITIN- LIKE PROTEIN SMT3A, SMT3A
 
Molecule 3 - RAN GTPASE-ACTIVATING PROTEIN 1
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSMT3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 419-587
    GeneKIAA1835, RANGAP1, SD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRANGAP1
 
Molecule 4 - E3 SUMO-PROTEIN LIGASE RANBP2
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSMT3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2631-2695
    GeneNUP358, RANBP2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMOTIF II OF RANBP2 IR1 WAS MUTATED TO IR2 MOTIF II
    Synonym358 KDA NUCLEOPORIN, NUCLEAR PORE COMPLEX PROTEIN NUP358, NUCLEOPORIN NUP358, RAN-BINDING PROTEIN 2, RANBP2, P270

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CSD3Mod. Amino Acid3-SULFINOALANINE

(-) Sites  (0, 0)

(no "Site" information available for 3UIO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:68 -Pro A:69
2Glu A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047508D16NSUMO2_HUMANPolymorphism17850328BD16N

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC9_HUMAN7-146  1A:7-146
2UBIQUITIN_2PS50053 Ubiquitin domain profile.SUMO2_HUMAN16-93  1B:16-93
3UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC9_HUMAN82-97  1A:82-97

(-) Exons   (13, 13)

Asymmetric/Biological Unit (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002831951bENSE00001427934chr2:109335937-109336134198RBP2_HUMAN1-24240--
1.3aENST000002831953aENSE00001628671chr2:109345588-10934565568RBP2_HUMAN25-47230--
1.5bENST000002831955bENSE00001658463chr2:109347230-109347341112RBP2_HUMAN47-84380--
1.6aENST000002831956aENSE00001642732chr2:109347778-109347930153RBP2_HUMAN85-135510--
1.7bENST000002831957bENSE00001779112chr2:109351988-109352218231RBP2_HUMAN136-212770--
1.8ENST000002831958ENSE00001730926chr2:109352560-109352705146RBP2_HUMAN213-261490--
1.9ENST000002831959ENSE00001785652chr2:109356945-109357137193RBP2_HUMAN261-325650--
1.10ENST0000028319510ENSE00001713500chr2:109363167-10936325488RBP2_HUMAN326-355300--
1.11aENST0000028319511aENSE00001718980chr2:109365376-109365585210RBP2_HUMAN355-425710--
1.12ENST0000028319512ENSE00001776974chr2:109367720-109367901182RBP2_HUMAN425-485610--
1.13aENST0000028319513aENSE00001779700chr2:109367984-109368159176RBP2_HUMAN486-544590--
1.13eENST0000028319513eENSE00001761857chr2:109368327-109368450124RBP2_HUMAN544-585420--
1.14bENST0000028319514bENSE00001718984chr2:109369454-109369615162RBP2_HUMAN586-639540--
1.15ENST0000028319515ENSE00001757154chr2:109369882-109370019138RBP2_HUMAN640-685460--
1.16ENST0000028319516ENSE00001624597chr2:109370281-109370427147RBP2_HUMAN686-734490--
1.17ENST0000028319517ENSE00001686256chr2:109371361-109371540180RBP2_HUMAN735-794600--
1.18ENST0000028319518ENSE00001591933chr2:109371632-10937171584RBP2_HUMAN795-822280--
1.19ENST0000028319519ENSE00001791450chr2:109374869-109375004136RBP2_HUMAN823-868460--
1.20ENST0000028319520ENSE00001684879chr2:109378557-10937865195RBP2_HUMAN868-899320--
1.21aENST0000028319521aENSE00001147357chr2:109379693-1093848445152RBP2_HUMAN900-261717180--
1.22ENST0000028319522ENSE00001009418chr2:109388157-109388327171RBP2_HUMAN2617-2674581D:2630-267445
1.23ENST0000028319523ENSE00001009429chr2:109388945-10938903793RBP2_HUMAN2674-2705321D:2674-269421
1.24ENST0000028319524ENSE00001291545chr2:109389324-109389502179RBP2_HUMAN2705-2764600--
1.25ENST0000028319525ENSE00001009419chr2:109392188-109392392205RBP2_HUMAN2765-2833690--
1.26ENST0000028319526ENSE00001009428chr2:109393586-109393687102RBP2_HUMAN2833-2867350--
1.27ENST0000028319527ENSE00001377207chr2:109397725-109397885161RBP2_HUMAN2867-2920540--
1.28ENST0000028319528ENSE00001383394chr2:109398584-109398857274RBP2_HUMAN2921-3012920--
1.29ENST0000028319529ENSE00001147257chr2:109398984-109399318335RBP2_HUMAN3012-31231120--
1.30bENST0000028319530bENSE00001316371chr2:109400052-1094022672216RBP2_HUMAN3124-32241010--

2.3ENST000003562443ENSE00001525423chr22:41682255-41681990266RAGP1_HUMAN-00--
2.6eENST000003562446eENSE00002184389chr22:41677086-41676937150RAGP1_HUMAN1-38380--
2.7aENST000003562447aENSE00000655593chr22:41670731-41670604128RAGP1_HUMAN38-80430--
2.8ENST000003562448ENSE00002178724chr22:41664160-4166410160RAGP1_HUMAN81-100200--
2.9bENST000003562449bENSE00000655579chr22:41660847-41660668180RAGP1_HUMAN101-160600--
2.10ENST0000035624410ENSE00000655571chr22:41657584-41657450135RAGP1_HUMAN161-205450--
2.11ENST0000035624411ENSE00000655562chr22:41654110-41653952159RAGP1_HUMAN206-258530--
2.12ENST0000035624412ENSE00000655554chr22:41652828-41652715114RAGP1_HUMAN259-296380--
2.13ENST0000035624413ENSE00001388340chr22:41652294-41652195100RAGP1_HUMAN297-330340--
2.14ENST0000035624414ENSE00002167356chr22:41652109-4165202585RAGP1_HUMAN330-358290--
2.15ENST0000035624415ENSE00001615125chr22:41650498-41650312187RAGP1_HUMAN358-420630--
2.16bENST0000035624416bENSE00001786527chr22:41648995-41648876120RAGP1_HUMAN421-460401C:432-46029
2.17bENST0000035624417bENSE00001635042chr22:41647113-41647011103RAGP1_HUMAN461-495351C:461-49535
2.18ENST0000035624418ENSE00001708342chr22:41645821-4164573389RAGP1_HUMAN495-524301C:495-52430
2.19ENST0000035624419ENSE00001792763chr22:41645455-41645334122RAGP1_HUMAN525-565411C:525-56541
2.20cENST0000035624420cENSE00001563055chr22:41642676-416416151062RAGP1_HUMAN565-587231C:565-58723

3.2bENST000003975152bENSE00001529011chr16:1359636-1359774139UBC9_HUMAN-00--
3.3cENST000003975153cENSE00001529008chr16:1362348-1362604257UBC9_HUMAN-00--
3.4bENST000003975154bENSE00002200477chr16:1364021-136409777UBC9_HUMAN1-22221A:3-2220
3.5ENST000003975155ENSE00000665751chr16:1364294-136437784UBC9_HUMAN23-50281A:23-5028
3.6aENST000003975156aENSE00000873575chr16:1365655-136572773UBC9_HUMAN51-75251A:51-7525
3.7ENST000003975157ENSE00000873577chr16:1370175-1370284110UBC9_HUMAN75-111371A:75-11137
3.8aENST000003975158aENSE00001287298chr16:1370439-137051880UBC9_HUMAN112-138271A:112-13827
3.9cENST000003975159cENSE00001287274chr16:1374731-13770192289UBC9_HUMAN138-158211A:138-15821

(-) 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:156
 aligned with UBC9_HUMAN | P63279 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
          UBC9_HUMAN      3 GIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS  158
               SCOP domains d3uioa_ A: Ubiquitin conjugating enzyme, UBC                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eeee................hhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: A:7-146 UniProt: 7-146                                                                                           ------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------UBIQUITIN_CONJUG------------------------------------------------------------- PROSITE (3)
           Transcript 3 (1) Exon 3.4b           Exon 3.5  PDB: A:23-50      Exon 3.6a  PDB: A:51-75  ------------------------------------Exon 3.8a  PDB: A:112-138  -------------------- Transcript 3 (1)
           Transcript 3 (2) ------------------------------------------------------------------------Exon 3.7  PDB: A:75-111              --------------------------Exon 3.9c             Transcript 3 (2)
                3uio A    3 GIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVcLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYcQNRVEYEKRVRAQAKKFAPS  158
                                    12        22        32        42        52        62        72        82        92|      102       112       122       132     | 142       152      
                                                                                                                     93-CSD                                      138-CSD                

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with SUMO2_HUMAN | P61956 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:79
                                    24        34        44        54        64        74        84         
         SUMO2_HUMAN     15 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   93
               SCOP domains d3uiob_ B: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee....hhhhhhhhhhhhh.....eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) -N----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -UBIQUITIN_2  PDB: B:16-93 UniProt: 16-93                                       PROSITE (2)
                 Transcript ------------------------------------------------------------------------------- Transcript
                3uio B   15 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   93
                                    24        34        44        54        64        74        84         

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with RAGP1_HUMAN | P46060 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:156
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581      
         RAGP1_HUMAN    432 ADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV  587
               SCOP domains d3uioc_ C: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..............hhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.16b  PDB: C:432-460   Exon 2.17b  PDB: C:461-495         -----------------------------Exon 2.19  PDB: C:525-565                ---------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------Exon 2.18  PDB: C:495-524     ----------------------------------------Exon 2.20c              Transcript 2 (2)
                3uio C  432 ADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV  587
                                   441       451       461       471       481       491       501       511       521       531       541       551       561       571       581      

Chain D from PDB  Type:PROTEIN  Length:65
 aligned with RBP2_HUMAN | P49792 from UniProtKB/Swiss-Prot  Length:3224

    Alignment length:65
                                  2639      2649      2659      2669      2679      2689     
          RBP2_HUMAN   2630 DDVLIVYELTPTAEQKALATKLKLPPTFFCYKNRPDYVSEEEEDDEDFETAVKKLNGKLYLDGSE 2694
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...hhhhhhhh............hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.22  PDB: D:2630-2674 [INCOMPLETE]     -------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.23             Transcript 1 (2)
                3uio D 2630 LDVLIVYELTPTVEEKAKADTLKLPPTFFcYKNRPDYVSEEEEDDEDFETAVKKLNGKLYLDGSE 2694
                                  2639      2649      2659      2669      2679      2689     
                                                      2659-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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UIO)

(-) Gene Ontology  (86, 114)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UBC9_HUMAN | P63279)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043398    HLH domain binding    Interacting selectively and non-covalently with Helix Loop Helix, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization.
    GO:0071535    RING-like zinc finger domain binding    Interacting selectively and non-covalently with a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain.
    GO:0061656    SUMO conjugating enzyme activity    Isoenergetic transfer of SUMO from one protein to another via the reaction X-SUMO + Y -> Y-SUMO + X, where both the X-SUMO and Y-SUMO linkages are thioester bonds between the C-terminal amino acid of SUMO and a sulfhydryl side group of a cysteine residue.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:1903755    positive regulation of SUMO transferase activity    Any process that activates or increases the frequency, rate or extent of SUMO transferase activity.
    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.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:1990356    sumoylated E2 ligase complex    A protein complex consisting of a SUMO (small ubiquitin-related modifier) protein bound to a SUMO-conjugating E2 ligase. Sumoylation of the E2 ligase is an intermediate step required for the formation of covalent bonds between a SUMO protein and its ultimate protein target. SUMO is transferred to the E2 ligase by a SUMO-activating E1 enzyme. Sumoylation of the target protein is either facilitated directly by the sumoylated E2 ligase or aided by an optional E3 ligase.
    GO:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
    GO:1990234    transferase complex    A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).

Chain B   (SUMO2_HUMAN | P61956)
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: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.
    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:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    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:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 C   (RAGP1_HUMAN | P46060)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0008536    Ran GTPase binding    Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
    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:0071375    cellular response to peptide hormone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:1904117    cellular response to vasopressin    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vasopressin stimulus.
    GO:0046826    negative regulation of protein export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    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.
    GO:0048678    response to axon injury    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 axon injury stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:1904115    axon cytoplasm    Any cytoplasm that is part of a axon.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:1990723    cytoplasmic periphery of the nuclear pore complex    Cytoplasm situated in close proximity to a nuclear pore complex.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

Chain D   (RBP2_HUMAN | P49792)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008536    Ran GTPase binding    Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0033132    negative regulation of glucokinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    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.
    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:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0090526    regulation of gluconeogenesis involved in cellular glucose homeostasis    Any process that modulates the frequency, rate or extent of gluconeogenesis as an integral part of cellular glucose homeostasis.
    GO:0010827    regulation of glucose transport    Any process that modulates the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    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:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    GO:0044615    nuclear pore nuclear basket    A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component.
    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
        RAGP1_HUMAN | P460601z5s 2grn 2gro 2grp 2grq 2grr 2io2 2io3 2iy0 3uin 3uip 5d2m
        RBP2_HUMAN | P497921rrp 1xke 1z5s 2las 3uin 3uip 4ga0 4i9y 4l6e 4lqw 5cll 5clq
        SUMO2_HUMAN | P619561wm2 1wm3 1wz0 1z5q 2awt 2ckh 2d07 2io0 2io3 2iyd 2n1w 2n9e 2rpq 3uin 3zo5 4bkg 4npn 5d2m 5elu 5eql 5ghb 5ghc
        UBC9_HUMAN | P632791a3s 1kps 1z5q 1z5s 2grn 2gro 2grp 2grq 2grr 2o25 2pe6 2px9 2xwu 3a4s 3uin 3uip 4w5v 4y1l 5d2m 5f6d 5f6e 5f6u 5f6v 5f6w 5f6x 5f6y 5fq2

(-) Related Entries Specified in the PDB File

1z5s 3uin 3uip