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(-) Description

Title :  CRYSTAL STRUCTURE OF D-63 FROM SULFOLOBUS SPINDLE VIRUS 1
 
Authors :  P. Kraft, D. Kummel, A. Oeckinghaus, G. H. Gauss, B. Wiedenheft, M. Young, C. M. Lawrence
Date :  05 Mar 04  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sulfolobus Spindle Virus, Ssv, Archaeal, Crenarchaeal, Helix-Turn-Helix, Four Helix Bundle, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kraft, A. Oeckinghaus, G. H. Gauss, B. Wiedenheft, M. Young, C. M. Lawrence
Structure Of D-63 From Sulfolobus Spindle-Shaped Virus 1: Surface Properties Of The Dimeric Four-Helix Bundle Suggest An Adaptor Protein Function
J. Virol. V. 78 7438 2004
PubMed-ID: 15220417  |  Reference-DOI: 10.1128/JVI.78.14.7438-7442.2004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 7.5 KDA PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: D-63
    Organism Scientific: SULFOLOBUS VIRUS 1
    Organism Taxid: 244589
    Synonym: ORF D-63

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1SKV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SKV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SKV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SKV)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1SKV)

(-) 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:64
 aligned with D63_SSV1 | P20215 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:64
                                                                                        63  
                                    11        21        31        41        51        61 |  
              D63_SSV1    2 SKEVLEKELFEMLDEDVRELLSLIHEIKIDRITGNMDKQKLGKAYFQVQKIEAELYQLIKVS--  -
               SCOP domains d1skva_ A: Hypothetical protein D-63                             SCOP domains
               CATH domains 1skvA00 A:2-65 Helix hairpin bin                                 CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  1skv A  2 SKEVLEKELFEmLDEDVRELLSLIHEIKIDRITGNmDKQKLGKAYFQVQKIEAELYQLIKVSHH 65
                                    11 |      21        31     |  41        51        61    
                                      13-MSE                  37-MSE                        


Chain B from PDB  Type:PROTEIN  Length:61
 aligned with D63_SSV1 | P20215 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:61
                                                                                    63   
                                    15        25        35        45        55       | - 
              D63_SSV1    6 LEKELFEMLDEDVRELLSLIHEIKIDRITGNMDKQKLGKAYFQVQKIEAELYQLIKVS---  -
               SCOP domains d1skvb_ B: Hypothetical protein D-63                          SCOP domains
               CATH domains 1skvB00 B:6-66 Helix hairpin bin                              CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  1skv B  6 LEKELFEmLDEDVRELLSLIHEIKIDRITGNmDKQKLGKAYFQVQKIEAELYQLIKVSHHH 66
                                   |15        25        35 |      45        55        65 
                                  13-MSE                  37-MSE                         


Chain C from PDB  Type:PROTEIN  Length:58
 aligned with D63_SSV1 | P20215 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:58
                                                                                   63 
                                    16        26        36        46        56      | 
              D63_SSV1    7 EKELFEMLDEDVRELLSLIHEIKIDRITGNMDKQKLGKAYFQVQKIEAELYQLIKVS-  -
               SCOP domains d1skvc_ C: Hypothetical protein D-63                       SCOP domains
               CATH domains 1skvC00 C:7-64 Helix hairpin bin                           CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  1skv C  7 EKELFEmLDEDVRELLSLIHEIKIDRITGNmDKQKLGKAYFQVQKIEAELYQLIKVSH 64
                                  | 16        26        36|       46        56        
                                 13-MSE                  37-MSE                       


Chain D from PDB  Type:PROTEIN  Length:56
 aligned with D63_SSV1 | P20215 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:65
                                                                                        63   
                                    11        21        31        41        51        61 |   
              D63_SSV1    2 SKEVLEKELFEMLDEDVRELLSLIHEIKIDRITGNMDKQKLGKAYFQVQKIEAELYQLIKVS---  -
               SCOP domains d1skvd_ D: Hypothetical prot         ein D-63                     SCOP domains
               CATH domains 1skvD00 D:2-66 Helix hairpin          bin                         CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  1skv D  2 SKEVLEKELFEmLDEDVRELLSLIHEIK---------KQKLGKAYFQVQKIEAELYQLIKVSHHH 66
                                    11 |      21       | -       |41        51        61     
                                      13-MSE          29        39
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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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SKV)

(-) Gene Ontology  (0, 0)

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