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(-) Description

Title :  TRIM5 B-BOX2 AND COILED-COIL CHIMERA
 
Authors :  J. M. Wagner, G. Doss, O. Pornillos
Date :  25 Feb 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.26
Chains :  Asym. Unit :  A,B,C,D,F,K
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  C,F,K  (1x)
Keywords :  Tripartite Motif, Hiv, Viral Restriction, Trim, E3 Ligase, Self- Assembly, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Wagner, M. D. Roganowicz, K. Skorupka, S. L. Alam, D. E. Christensen, G. L. Doss, Y. Wan, G. A. Frank, B. K. Ganser-Pornillos, W. I. Sundquist, O. Pornillos
Mechanism Of B-Box 2 Domain-Mediated Higher-Order Assembly Of The Retroviral Restriction Factor Trim5 Alpha.
Elife V. 5 2016
PubMed-ID: 27253059  |  Reference-DOI: 10.7554/ELIFE.16309

(-) Compounds

Molecule 1 - TRIPARTITE MOTIF-CONTAINING PROTEIN 5, SERINE--TRNA LIGASE CHIMERA
    Chains: A, B, C, D, F, K
    EC Number: 6.3.2.-, 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: TRIM5, SERS, TT_C0520
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA, THERMUS THERMOPHILUS (STRAIN HB27 / ATCC BAA-163 / DSM 7039)
    Organism Taxid: 9544, 262724
    Strain: HB27 / ATCC BAA-163 / DSM 7039
    Synonym: TRIM5ALPHA,SERYL-TRNA SYNTHETASE,SERRS,SERYL-TRNA(SER/SEC) SYNTHETASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDFK
Biological Unit 1 (1x): AB D  
Biological Unit 2 (1x):   C FK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/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  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:108 , ASP A:111 , HIS A:125 , HIS A:128binding site for residue ZN A 701
02AC2SOFTWARECYS A:97 , HIS A:100 , CYS A:116 , CYS A:119binding site for residue ZN A 702
03AC3SOFTWARECYS B:108 , ASP B:111 , HIS B:125 , HIS B:128binding site for residue ZN B 701
04AC4SOFTWARECYS B:97 , HIS B:100 , CYS B:116 , CYS B:119binding site for residue ZN B 702
05AC5SOFTWARECYS C:108 , ASP C:111 , HIS C:125 , HIS C:128binding site for residue ZN C 701
06AC6SOFTWARECYS C:97 , HIS C:100 , CYS C:116 , CYS C:119binding site for residue ZN C 702
07AC7SOFTWARECYS D:108 , ASP D:111 , HIS D:125 , HIS D:128binding site for residue ZN D 701
08AC8SOFTWARECYS D:97 , HIS D:100 , CYS D:116 , CYS D:119binding site for residue ZN D 702
09AC9SOFTWARECYS F:108 , ASP F:111 , HIS F:125 , HIS F:128binding site for residue ZN F 701
10AD1SOFTWARECYS F:97 , HIS F:100 , CYS F:116 , CYS F:119binding site for residue ZN F 702
11AD2SOFTWARECYS K:108 , ASP K:111 , HIS K:125 , HIS K:128binding site for residue ZN K 701
12AD3SOFTWARECYS K:97 , HIS K:100 , CYS K:116 , CYS K:119binding site for residue ZN K 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IEA)

(-) 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:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea A  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179                                             


Chain B from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea B  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179                                             


Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea C  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179                                             


Chain D from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea D  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179                                             


Chain F from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea F  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179                                             


Chain K from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eeehhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5iea K  95 DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTALEMLRQKQQEAETERNQVAALIARGKALGEQTQYMRELISELEHRLQGSMMDLLQGVDGIIKRIE 224
                                   104       114       124       134       144       154       164 ||    186       196       206       216        
                                                                                                 166|                                             
                                                                                                  179
   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 5IEA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (43, 45)

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  TRIM5_MACMU | Q0PF16
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYS_THET2 | P34945: 1ser 1ses 1set 1sry 3err 5eiu 5f7t
        TRIM5_MACMU | Q0PF16: 2lm3 3uv9 4b3n 4tkp 5eiu 5f7t 5k3q

(-) Related Entries Specified in the PDB File

5eiu 5f7t