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(-) Description

Title :  MAMMALIAN CRYPTOCHROME IN COMPLEX WITH A SMALL MOLECULE COMPETITOR OF ITS UBIQUITIN LIGASE
 
Authors :  S. Nangle, W. Xing, N. Zheng
Date :  06 Sep 13  (Deposition) - 16 Oct 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Photolyase Homology Region, Transcriptional Repressor, Period, Fbxl3, Clock, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nangle, W. Xing, N. Zheng
Crystal Structure Of Mammalian Cryptochrome In Complex With A Small Molecule Competitor Of Its Ubiquitin Ligase.
Cell Res. V. 23 1417 2013
PubMed-ID: 24080726  |  Reference-DOI: 10.1038/CR.2013.136

(-) Compounds

Molecule 1 - CRYPTOCHROME-2
    Chains: C, A, B, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: PHOTOLYASE HOMOLOGY REGION UNP RESIDUES 1-512
    Gene: CRY2, KIAA0658
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   C 
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
12CX4Ligand/IonN-[(2S)-3-(9H-CARBAZOL-9-YL)-2-HYDROXYPROPYL]-N-(FURAN-2-YLMETHYL)METHANESULFONAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12CX1Ligand/IonN-[(2S)-3-(9H-CARBAZOL-9-YL)-2-HYDROXYPROPYL]-N-(FURAN-2-YLMETHYL)METHANESULFONAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12CX1Ligand/IonN-[(2S)-3-(9H-CARBAZOL-9-YL)-2-HYDROXYPROPYL]-N-(FURAN-2-YLMETHYL)METHANESULFONAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12CX1Ligand/IonN-[(2S)-3-(9H-CARBAZOL-9-YL)-2-HYDROXYPROPYL]-N-(FURAN-2-YLMETHYL)METHANESULFONAMIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
12CX1Ligand/IonN-[(2S)-3-(9H-CARBAZOL-9-YL)-2-HYDROXYPROPYL]-N-(FURAN-2-YLMETHYL)METHANESULFONAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN C:307 , TRP C:310 , HIS C:373 , ARG C:376 , HIS C:377 , PHE C:399 , VAL C:410 , SER C:414 , TRP C:415 , TRP C:417 , HOH C:1343 , HOH C:1397BINDING SITE FOR RESIDUE 2CX C 900
2AC2SOFTWAREGLN A:307 , TRP A:310 , HIS A:373 , ARG A:376 , HIS A:377 , PHE A:399 , VAL A:410 , SER A:414 , TRP A:415 , TRP A:417 , HOH A:1343 , HOH A:1399BINDING SITE FOR RESIDUE 2CX A 900
3AC3SOFTWAREGLN B:307 , TRP B:310 , HIS B:373 , ARG B:376 , HIS B:377 , PHE B:399 , VAL B:410 , SER B:414 , TRP B:415 , TRP B:417BINDING SITE FOR RESIDUE 2CX B 900
4AC4SOFTWAREGLN D:307 , TRP D:310 , HIS D:373 , ARG D:376 , HIS D:377 , PHE D:399 , VAL D:410 , SER D:414 , TRP D:415 , TRP D:417 , HOH D:1299BINDING SITE FOR RESIDUE 2CX D 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MLP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MLP)

(-) 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:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4mlpa1 A:21-223 automated matches                                                                                                                                                                         d4mlpa2 A:224-512 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.........hhhhhhhhh...eeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhh......hhhhhhhhhhh...........hhhhhh........hhhhhhh..hhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mlp A  21 ASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY 512
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510  


Chain B from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4mlpb1 B:21-223 automated matches                                                                                                                                                                         d4mlpb2 B:224-512 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhh...eeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhh......hhhhhhhhhhh...........hhhhhhhh......hhhhhhh..hhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mlp B  21 ASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY 512
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510  


Chain C from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4mlpc1 C:21-223 automated matches                                                                                                                                                                         d4mlpc2 C:224-512 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.........hhhhhhhhh...eeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhh......hhhhhhhhhhh...........hhhhhhh.......hhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mlp C  21 ASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY 512
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510  


Chain D from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4mlpd1 D:21-223 automated matches                                                                                                                                                                         d4mlpd2 D:224-512 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhh...eeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhh......hhhhhhhhhhh...........hhhhhhhh......hhhhhhh..hhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mlp D  21 ASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY 512
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        CRY2_MOUSE | Q9R194: 4i6e 4i6g 4i6j 4u8h

(-) Related Entries Specified in the PDB File

4i6e APO MCRY2
4i6g FAD-BOUND MCRY2
4i6j UBIQUITIN LIGASE (FBXL3) BOUND MCRY2