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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CUL2-RBX1-ELOBC-VHL UBIQUITIN LIGASE COMPLEX
 
Authors :  T. A. F. Cardote, M. S. Gadd, A. Ciulli
Date :  11 Feb 17  (Deposition) - 07 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.90
Chains :  Asym./Biol. Unit :  A,B,C,R,V
Keywords :  Cullin Ring, E3 Ubiquitin Ligase, Vhl, Ligase, Cullin-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. F. Cardote, M. S. Gadd, A. Ciulli
Crystal Structure Of The Cul2-Rbx1-Elobc-Vhl Ubiquitin Ligase Complex.
Structure V. 25 901 2017
PubMed-ID: 28591624  |  Reference-DOI: 10.1016/J.STR.2017.04.009

(-) Compounds

Molecule 1 - CULLIN-2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: CUL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CUL-2
 
Molecule 2 - VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
    Chains: V
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VHL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN G7,PVHL
 
Molecule 3 - E3 UBIQUITIN-PROTEIN LIGASE RBX1
    Chains: R
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: RBX1, RNF75, ROC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN ZYP,RING FINGER PROTEIN 75,RING-BOX PROTEIN 1,RBX1, REGULATOR OF CULLINS 1
 
Molecule 4 - ELONGIN-B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ELOB, TCEB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELOB,ELONGIN 18 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B,SIII P18,TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
 
Molecule 5 - ELONGIN-C
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ELOC, TCEB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELOC,ELONGIN 15 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C,SIII P15,TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCRV

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS R:42 , CYS R:45 , HIS R:80 , CYS R:83binding site for residue ZN R 201
2AC2SOFTWARECYS R:53 , CYS R:56 , CYS R:68 , HIS R:82binding site for residue ZN R 202
3AC3SOFTWARECYS R:75 , HIS R:77 , CYS R:94 , ASP R:97binding site for residue ZN R 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N4W)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Tyr A:49 -Pro A:50
2Glu A:174 -Asp A:175
3Gly A:360 -Asp A:361
4Ser A:383 -Val A:384
5Val A:384 -Cys A:385
6Val R:38 -Val R:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N4W)

(-) Exons   (0, 0)

(no "Exon" information available for 5N4W)

(-) 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:671
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..................hhhhhhhhhhhh...eeeee..............................................hhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhh...ee.........ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n4w A   1 MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKNDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPSVCKAPELLAKYCDNLLKKSAGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTVSFQIYVLQAGAWPLTQAPPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNLKPVAMVTTYQMAVSEVSYKELQDSTQMNEKELTKTISLLDVKMINESSFSLNMNFTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKYIERSQASADEYSYVA 745
                                    10        20        30        40        50        60        70        80        90       100       110     ||138       148       158       168       178       188    || 202       212       222       232       242       252       262       272       282       293       303       313       323       333       343       353       363       373       384       394       405       415       425       435       445       455       465       475       485       495    || 510       520  ||   536       546       556       566|||||  579    |||596       606       617      |637      |663       673       683       693       703       713       723    || 734       744 
                                                                                                                                             116|                                                       193|                                                                                         290|                                                                                      381|                 403|                                                                                            500|              523|                                  567||||       584|||                 614|     624|      644|                                                                728|               
                                                                                                                                              135                                                        198                                                                                          292                                                                                       383                  405                                                                                             506               530                                   569|||        591||                  616      635       661                                                                 730               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              571||         592|                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               572|          594                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                574                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhh.hhh.ee.............................ee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 5n4w B   1 MDVFLMIRRTTIFTDSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECSQTARPQAPATLAFRADDTFEAPFSSPP  97
                                    12    ||  26        36        46        56   ||   69    ||  81     || 95  
                                    9|   17|                                    60|        74|        87|     
                                    12    22                                     64         77         92     


Chain C from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eehhhhhh.hhhhhhhhh......ee.....hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 5n4w C  17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQANEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46    ||| 61        71        81        91       101       111 
                                                             51||                                                      
                                                              53|                                                      
                                                               58                                                      


Chain R from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee..................hhhhhhhh.........ee.......eehhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 5n4w R  17 AKKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE 102
                                    26        36        46        56        66        76        86        96      


Chain V from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 5n4w V 157 TLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPN 193
                                   166       176       186
   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  (0, 0)

(no "SCOP Domain" information available for 5N4W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N4W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N4W)

(-) Gene Ontology  (78, 128)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:174 - Asp A:175   [ RasMol ]  
    Gly A:360 - Asp A:361   [ RasMol ]  
    Ser A:383 - Val A:384   [ RasMol ]  
    Tyr A:49 - Pro A:50   [ RasMol ]  
    Val A:384 - Cys A:385   [ RasMol ]  
    Val R:38 - Val R:39   [ RasMol ]  
 

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  VHL_HUMAN | P40337
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 Related Entries

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

UniProtKB/Swiss-Prot
        CUL2_HUMAN | Q13617: 4wqo
        ELOB_HUMAN | Q15370: 1lm8 1lqb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5t35
        ELOC_HUMAN | Q15369: 1lm8 1lqb 1vcb 2c9w 2izv 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5t35
        RBX1_HUMAN | P62877: 1ldj 1ldk 1u6g 2hye 2lgv 3dpl 3dqv 3rtr 4f52 4p5o
        VHL_HUMAN | P40337: 1lm8 1lqb 1vcb 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5lli 5t35

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5N4W)