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(-) Description

Title :  STRUCTURE OF A GLOMULIN-RBX1-CUL1 COMPLEX
 
Authors :  D. M. Duda, J. L. Olszewski, B. A. Schulman
Date :  11 May 12  (Deposition) - 19 Sep 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Cullin-Ring E3 Ligase, Inhibitor, Cell Cycle-Ligase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Duda, J. L. Olszewski, A. E. Tron, M. Hammel, L. J. Lambert, M. B. Waddell, T. Mittag, J. A. Decaprio, B. A. Schulman
Structure Of A Glomulin-Rbx1-Cul1 Complex: Inhibition Of A Ring E3 Ligase Through Masking Of Its E2-Binding Surface.
Mol. Cell V. 47 371 2012
PubMed-ID: 22748924  |  Reference-DOI: 10.1016/J.MOLCEL.2012.05.044

(-) Compounds

Molecule 1 - CULLIN-1
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 511693
    Fragment: C-TERMINAL DOMAIN, DELTA WHB DOMAIN, UNP RESIDUES 411-690
    Gene: CUL1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CUL-1
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE RBX1
    Chains: B, D
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 5-108
    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 3 - GLOMULIN
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLMN, FAP48, FAP68, VMGLOM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FK506-BINDING PROTEIN-ASSOCIATED PROTEIN, FAP, FKBP- ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:42 , CYS B:45 , HIS B:80 , CYS B:83BINDING SITE FOR RESIDUE ZN B 201
2AC2SOFTWARECYS B:75 , HIS B:77 , CYS B:94 , ASP B:97BINDING SITE FOR RESIDUE ZN B 202
3AC3SOFTWARECYS B:53 , CYS B:56 , CYS B:68 , HIS B:82BINDING SITE FOR RESIDUE ZN B 203
4AC4SOFTWARECYS D:42 , CYS D:45 , HIS D:80 , CYS D:83BINDING SITE FOR RESIDUE ZN D 201
5AC5SOFTWARECYS D:75 , HIS D:77 , CYS D:94 , ASP D:97BINDING SITE FOR RESIDUE ZN D 202
6AC6SOFTWARECYS D:53 , CYS D:56 , CYS D:68 , HIS D:82BINDING SITE FOR RESIDUE ZN D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F52)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys E:53 -Asn E:54
2Met F:168 -Asp F:169
3Leu F:456 -Pro F:457
4Leu F:494 -Trp F:495

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F52)

(-) Exons   (0, 0)

(no "Exon" information available for 4F52)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.......eeeeehhhhhhhhhhhh..eeehhhhhhhhh.hhhhhhhhhhhhhhh..ee.................eeee.........eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f52 A 420 EELARYCDSLLKLEDTLNQVMEKFKKDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMK 689
                                   429 ||    449     ||461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681        
                                     431|          455|                                                                                                                                                                                                                                       
                                      442           458                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains d4f52b_ B: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee.................hhhhhh..........eee.....eeehhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4f52 B  20 KRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ 104
                                    29        39        49        59      ||70        80        90       100    
                                                                         66|                                    
                                                                          68                                    


Chain C from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..............hhhhhhhhhhhhhhhhhhh...eeee.hhh.eeeeee.......eeeeehhhhhhhhhhhh..eeehhhhhhhhh.hhhhhhhhhhhhhhh..eee................eeee.........eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f52 C 419 PEELARYCDSLLKLEDTLNQVMEKFKKIVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPM 688
                                   428  ||   448       462       472       482       492 ||    504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684    
                                      431|           456|                              494|                                                                                                                                                                                               
                                       442            461                               497                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains d4f52d_ D: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee..................hhhhhhh..........eee.....eeehhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4f52 D  20 KRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ 104
                                    29        39        49        59        69        79        89        99     


Chain E from PDB  Type:PROTEIN  Length:523
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f52 E   1 MAVEELQSIIKRCQILEGLFQLAGQRCIEEGHTDQLLEIIQNEKNKVIIKNMGWNLVGPVVRCLLCKDKEDSKRKVYFLIFDLLVKLCNPKELLLGLLELIEEPSGKQISQSILLLLQPLQTVIQKLHNKAYSIGLALSTLWNQLSLLPVPYSKMDDYGLCQCCKALIEFTKPFVEEVIDNKENSLENEKLKDELLKFCFKSLKCPLLTAQFFDPFRYFASEIIGFLSAIGHPFPKMKQLADSMASLAYLVFVQGIHIDQLPMVLSPLYLLQFNMGHIEVFLQRTEESVISKGLELLENSLLRIEDNSLLYQYLEIKSFLTVPQGLVKVMTLCPIETLRKKSLAMLQLYINKLDSQGKYTLFRCLLNTSNHSGVEAFIIQNIKNQIDMSLKRKWFTGPQLISLLDLVLFLPEGAETDLLQNSDRIMASLNLLRYLVIKDNENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKSKDPPEMQLKVLHSALFTFDLIESVLARVEELIEIKT 583
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159   ||  173       183       193       203       213       223  ||   241       251      |282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432 ||    446       456       466       476       486       496       506       516       526       550       560       570       580   
                                           17|                                                                                                                                     163|                                                       226|                    258|                                                                                                                                                       434|                                                                                             535|                                 
                                            27                                                                                                                                      168                                                        235                     280                                                                                                                                                        439                                                                                              550                                 


Chain F from PDB  Type:PROTEIN  Length:512
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f52 F   1 MAVEELQSIIKRCQILEEQKEEDFGLFQLAGQRCIEELLEIIQNEKNKVIIKNMGWNLVGPVVRCLLCSKRKVYFLIFDLLVKLCNPKELLLGLLELIEEPSGKQISQSILLLLQPLQTVIQKLHNKAYSIGLALSTLWNQLSLLPVPYQIQMDDYGLCQCCKALIEFTKPFVEEVIDNEKLKDELLKFCFKSLKCPLLTAQFFNDPFRYFASEIIGFLSAIGHPFPKMINKQLADSMASLAYLVFVQGIHIDQLPMVLSPLYLLQFNMGHIEVFLQRTEESVISKGLELLENSLLRIEDNSLLYQYLEIKSFLTVPQGLVKVMTLCPIETLRKKSLAMLQLYINKLDSQGKYTLFRCLLNTSNHSGVEAFIIQNIKNQIDMSLKWFTGPQLISLLDLVLFLPEGAETDLLQNSDRIMASLNLLRYLVIKDNENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKPPEMQLKVLHSALFTFDLIESVLARVEELIEIKT 583
                                    10        22        32      ||47        57        67       |82        92       102       112       122       132       142       152       165       175       185       202       212       222   ||  239       249       259|      288       298       308       318       328       338       348       358       368       378       388       398       408       418       428   ||  444       454       464       474       484       494       504       514       524       551       561       571       581  
                                             19|               39|                            75|                                                                             161|                         193|                      226|                      259|                                                                                                                                                      432|                                                                                          532|                                 
                                              22                45                             81                                                                              165                          201                       234                       279                                                                                                                                                       439                                                                                           550
   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, 2)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F52)

(-) Gene Ontology  (80, 102)

Asymmetric Unit(hide GO term definitions)

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  4f52
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  CUL1_HUMAN | Q13616
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  GLMN_HUMAN | Q92990
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  RBX1_HUMAN | P62877
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 Related Entries

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

UniProtKB/Swiss-Prot
        CUL1_HUMAN | Q13616: 1ldj 1ldk 1u6g 3rtr 3tdu 3tdz 4p5o 5v89
        RBX1_HUMAN | P62877: 1ldj 1ldk 1u6g 2hye 2lgv 3dpl 3dqv 3rtr 4p5o 5n4w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4F52)