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(-) Description

Title :  CRYSTAL STRUCTURE OF UBR-BOX FROM UBR6 IN A DOMAIN-SWAPPING CONFORMATION
 
Authors :  J. Munoz-Escobar, G. Kozlov, K. Gehring
Date :  27 Apr 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Domain Swapping, Zinc Finger, Zinc, Ubr-Box, Ubr6, Fbxo11, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Munoz-Escobar, G. Kozlov, K. Gehring
Crystal Structure Of Ubr-Box From Ubr6/Fbxo11 Reveals A Domain Swapping Mediated By Zinc Coordination
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - F-BOX ONLY PROTEIN 11
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System Taxid511693
    GeneFBXO11, FBX11, PRMT9, VIT1, UG063H01
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN ARGININE N-METHYLTRANSFERASE 9, VITILIGO-ASSOCIATED PROTEIN 1, VIT-1, UBR6/FBXO11

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2ZN14Ligand/IonZINC ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:848 , HIS A:883 , HIS C:848 , HIS C:883binding site for residue ZN A 1001
02AC2SOFTWARECYS A:865 , CYS A:868 , CYS C:888 , CYS D:835binding site for residue ZN A 1002
03AC3SOFTWARECYS A:868 , CYS A:872 , CYS C:890 , CYS C:899binding site for residue ZN A 1003
04AC4SOFTWARECYS A:853 , CYS A:856 , HIS A:873 , HIS A:876binding site for residue ZN A 1004
05AC5SOFTWARECYS A:890 , CYS A:899 , CYS C:868 , CYS C:872binding site for residue ZN A 1005
06AC6SOFTWARETYR A:837 , ILE A:839binding site for residue EDO A 1006
07AC7SOFTWAREILE A:869 , LYS A:870 , HIS A:873 , GLN A:874 , GLY A:875 , ASN B:897 , THR D:855binding site for residue EDO A 1007
08AC8SOFTWAREHIS A:848 , ASP A:849 , ARG C:885binding site for residue EDO A 1008
09AC9SOFTWAREASP A:877 , VAL A:878 , GLN D:874 , GLY D:875binding site for residue EDO A 1009
10AD1SOFTWAREHIS B:848 , HIS B:883 , EDO B:1006 , HIS D:848 , HIS D:883binding site for residue ZN B 1001
11AD2SOFTWARECYS B:853 , CYS B:856 , HIS B:873 , HIS B:876binding site for residue ZN B 1002
12AD3SOFTWARECYS B:865 , CYS B:868 , CYS C:835 , CYS D:888binding site for residue ZN B 1003
13AD4SOFTWARECYS B:868 , CYS B:872 , CYS D:890 , CYS D:899binding site for residue ZN B 1004
14AD5SOFTWARECYS B:890 , CYS B:899 , CYS D:868 , CYS D:872binding site for residue ZN B 1005
15AD6SOFTWAREHIS B:883 , ASP B:884 , ZN B:1001 , HIS D:848 , PHE D:850 , ALA D:863binding site for residue EDO B 1006
16AD7SOFTWARETYR A:845 , PRO B:846 , MET B:847 , HIS B:848 , ARG B:885 , ARG D:885 , HOH D:1116binding site for residue EDO B 1007
17AD8SOFTWARECYS A:888 , CYS B:835 , CYS C:865 , CYS C:868binding site for residue ZN C 1001
18AD9SOFTWARECYS C:853 , CYS C:856 , HIS C:873 , HIS C:876binding site for residue ZN C 1002
19AE1SOFTWAREHIS A:848 , PHE A:850 , ALA A:863 , HIS C:883 , ASP C:884 , PHE C:887binding site for residue EDO C 1003
20AE2SOFTWARECYS A:835 , CYS B:888 , CYS D:865 , CYS D:868binding site for residue ZN D 1001
21AE3SOFTWARECYS D:853 , CYS D:856 , HIS D:873 , HIS D:876binding site for residue ZN D 1002
22AE4SOFTWAREARG A:882 , ASP D:877binding site for residue EDO D 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VMD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VMD)

(-) 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:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeeee...........hhhhhhhhh....eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 5vmd A 834 QCLYKISSYTSYPMHDFYRCHTCNTTDRNAICVNCIKKCHQGHDVEFIRHDRFFCDCGAGTLSNPCTLA 902
                                   843       853       863       873       883       893         

Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhh.eeeeeee.........hhhhhhhh.....eeeeeee...hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5vmd B  -4 GPLGSGQCLYKISSYTSYPMHDFYRCHTCNDRNAICVNCIKKCHQGHDVEFIRHDRFFCDCGAGTLSNPCTL 901
                                || 837       847       857|      869       879       889       899  
                                0|                     857|                                         
                               833                      860                                         

Chain C from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhh.eeeeeee..........hhhhhhhh.....eeeeeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5vmd C  -4 GPLGSGQCLYKISSYTSYPMHDFYRCHTCNTDRNAICVNCIKKCHQGHDVEFIRHDRFFCDCGAGTLSNPCTL 901
                                || 837       847       857|      868       878       888       898   
                                0|                     857|                                          
                               833                      859                                          

Chain D from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhh.eeeeeee........hhhhhhhh.....eeeeeee...hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5vmd D 833 GQCLYKISSYTSYPMHDFYRCHTCNRNAICVNCIKKCHQGHDVEFIRHDRFFCDCGAGTLSNPCTL 901
                                   842       852    || 865       875       885       895      
                                                  857|                                        
                                                   861                                        

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  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 5VMD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5VMD)

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