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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  A UBIQUITIN LIGASE-SUBSTRATE COMPLEX
 
Authors :  W. Xing, L. Busino, T. R. Hinds, S. T. Marionni, N. H. Saifee, M. F. Bush, M N. Zheng
Date :  29 Nov 12  (Deposition) - 13 Mar 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Circadian Clock, Ubiquitination, Lrr, F-Box, Photolyase Fold, Periods, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Xing, L. Busino, T. R. Hinds, S. T. Marionni, N. H. Saifee, M. F. Bush, M. Pagano, N. Zheng
Scffbxl3 Ubiquitin Ligase Targets Cryptochromes At Their Cofactor Pocket.
Nature V. 496 64 2013
PubMed-ID: 23503662  |  Reference-DOI: 10.1038/NATURE11964

(-) Compounds

Molecule 1 - CRYPTOCHROME-2
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 1-544
    Gene: CRY2, KIAA0658
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - F-BOX/LRR-REPEAT PROTEIN 3
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: FBXL3, FBL3A, FBXL3A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 3A, F-BOX/LRR-REPEAT PROTEIN 3A
 
Molecule 3 - S-PHASE KINASE-ASSOCIATED PROTEIN 1
    Chains: C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYCLIN-A/CDK2-ASSOCIATED PROTEIN P19, ORGAN OF CORTI PROTEIN 2, OCP-2, ORGAN OF CORTI PROTEIN II, OCP-II, RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN, SIII, TRANSCRIPTION ELONGATION FACTOR B, P19A, P19SKP1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4I6J)

(-) Sites  (0, 0)

(no "Site" information available for 4I6J)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:430 -B:340

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro C:44 -Val C:45
2Val C:87 -Trp C:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I6J)

(-) Exons   (0, 0)

(no "Exon" information available for 4I6J)

(-) 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:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4i6ja1 A:21-225 automated matches                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........hhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhh......hhhhhhhhhhhh...........hhhhhh.....hhhhhhhh......................hhhhhhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6j A  21 ASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRYRGLCLLASVPSCVED 527
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250||     264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524   
                                                                                                                                                                                                                                                                251|                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                 256                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh..hhhhhhhhh..hhhhhh...hhhhh.eeeeee...........hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh........eeeeee...hhhhhhhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhh....eee.......hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh.......eeeeeee............hhhhhhhhhhhh...eeeeeee.................eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhh....eeee....eehhhhhhhhhhhhhhh.eeee....ee.....hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6j B  35 DWGNLLQDIILQVFKYLPLLDRAHASQVCRNWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESAEAACDILSQLVNCSLKTLGLISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLVANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSENPGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPRLVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLIPDQKYSLEQIHWEVSKHLGRVWFPDMMPTW 428
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424    


Chain C from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains d4i6jc1 C:3-64 automated matches                    d4i6jc2 C:85-162 automated matches                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........ee...........................hhhhhhhh..............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6j C   3 SIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDPVPLPNVNAAILKKVIQWCTHIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEE 162
                                    12        22        32||      52        62 ||     92       102       112       122       132       142       152       162
                                                         33|                  64|                                                                             
                                                          44                   85
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I6J)

(-) Gene Ontology  (63, 80)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro C:44 - Val C:45   [ RasMol ]  
    Val C:87 - Trp C:88   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CRY2_MOUSE | Q9R194: 4i6e 4i6g 4mlp 4u8h
        SKP1_HUMAN | P63208: 1fqv 1fs1 1fs2 1ldk 1p22 2ass 2ast 2e31 2e32 2ovp 2ovq 2ovr 3l2o 3wso 5ibk 5jh5 5k35

(-) Related Entries Specified in the PDB File

4i6e 4i6g