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(-) Description

Title :  CRYSTAL STRUCTURE OF RUBELLA VIRUS CAPSID PROTEIN (RESIDUES 127-277)
 
Authors :  V. Mangala Prasad, A. Fokine, M. G. Rossmann
Date :  27 Sep 12  (Deposition) - 11 Dec 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Partial Beta Barrel, Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Mangala Prasad, S. D. Willows, A. Fokine, A. J. Battisti, S. Sun, P. Plevka, T. C. Hobman, M. G. Rossmann
Rubella Virus Capsid Protein Structure And Its Role In Viru Assembly And Infection.
Proc. Natl. Acad. Sci. Usa V. 110 20105 2013
PubMed-ID: 24282305  |  Reference-DOI: 10.1073/PNAS.1316681110

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: CAPSID
    Organism Common: RUBV
    Organism Scientific: RUBELLA VIRUS
    Organism Taxid: 11043
    Strain: M33

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2LDA18Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LDA12Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LDA2Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LDA4Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR C:68BINDING SITE FOR RESIDUE LDA A 201
02AC2SOFTWARETRP A:94 , TYR A:101 , LEU A:116 , HOH A:307 , HOH A:313 , LEU C:51 , GLY C:52 , MET C:67BINDING SITE FOR RESIDUE LDA A 202
03AC3SOFTWARELDA A:205 , LDA A:206 , MET E:67 , TYR E:68 , TRP F:33 , PHE F:41BINDING SITE FOR RESIDUE LDA A 203
04AC4SOFTWAREMET A:67 , TYR A:68 , LDA A:205 , LDA A:206 , LDA A:207BINDING SITE FOR RESIDUE LDA A 204
05AC5SOFTWARELEU A:51 , PRO A:64 , LDA A:203 , LDA A:204 , TRP F:94 , GLY F:95 , LYS F:96BINDING SITE FOR RESIDUE LDA A 205
06AC6SOFTWAREMET A:67 , TYR A:68 , LDA A:203 , LDA A:204 , TRP B:33 , PHE B:41 , LDA B:206BINDING SITE FOR RESIDUE LDA A 206
07AC7SOFTWARELDA A:204BINDING SITE FOR RESIDUE LDA A 207
08AC8SOFTWARETRP A:31 , TRP A:33 , TYR A:101 , LEU A:116 , MET B:67 , TYR B:68 , LDA B:204BINDING SITE FOR RESIDUE LDA B 201
09AC9SOFTWAREHOH A:309 , HOH A:310BINDING SITE FOR RESIDUE CL B 202
10BC1SOFTWAREPRO B:64 , MET B:67 , LDA B:204 , TRP D:94 , GLY D:95 , LYS D:96BINDING SITE FOR RESIDUE LDA B 203
11BC2SOFTWARELDA B:201 , LDA B:203 , LDA B:205 , MET C:67 , TYR C:68 , PHE D:41 , LEU D:116BINDING SITE FOR RESIDUE LDA B 204
12BC3SOFTWARETYR B:68 , LDA B:204BINDING SITE FOR RESIDUE LDA B 205
13BC4SOFTWARELDA A:206 , TRP B:94 , LYS B:96 , TYR B:101 , LEU E:51 , MET E:67BINDING SITE FOR RESIDUE LDA B 206
14BC5SOFTWARETRP C:31 , TRP C:33 , PHE C:41 , MET D:67 , TYR D:68 , LDA F:202 , LDA F:203BINDING SITE FOR RESIDUE LDA D 201
15BC6SOFTWAREHOH C:204 , HOH C:209 , TYR D:83BINDING SITE FOR RESIDUE CL D 202
16BC7SOFTWARETYR D:68BINDING SITE FOR RESIDUE LDA D 203
17BC8SOFTWARETYR E:83 , HOH F:304 , HOH F:305 , HOH F:307BINDING SITE FOR RESIDUE CL E 201
18BC9SOFTWARELEU D:51 , GLY D:52 , PRO D:64 , MET D:67 , TRP E:94 , GLY E:95 , LYS E:96 , ARG E:99 , LDA F:203BINDING SITE FOR RESIDUE LDA E 202
19CC1SOFTWARETYR F:68BINDING SITE FOR RESIDUE LDA F 201
20CC2SOFTWARETRP C:94 , ARG C:99 , LDA D:201 , LEU F:51 , GLY F:52BINDING SITE FOR RESIDUE LDA F 202
21CC3SOFTWARELDA D:201 , TRP E:31 , TRP E:33 , PHE E:41 , LDA E:202 , MET F:67 , TYR F:68BINDING SITE FOR RESIDUE LDA F 203

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:27 -B:71
2A:71 -B:27
3C:27 -D:71
4C:71 -D:27
5E:27 -F:71
6E:71 -F:27

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:72 -Pro A:73
2Pro A:120 -Val A:121
3Gly B:72 -Pro B:73
4Gly C:72 -Pro C:73
5Gly C:123 -Leu C:124
6Thr D:24 -Glu D:25
7Gly D:72 -Pro D:73
8Gly E:72 -Pro E:73
9Pro E:120 -Val E:121
10Val F:121 -Arg F:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HAR)

(-) 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:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4har A  25 EACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVR 122
                                    34        44        54        64        74        84        94       104       114        


Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4har B  25 EACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPV 121
                                    34        44        54        64        74        84        94       104       114       


Chain C from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4har C  25 EACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVRGL 124
                                    34        44        54        64        74        84        94       104       114       124


Chain D from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4har D  24 TEACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVR 122
                                    33        43        53        63        73        83        93       103       113         


Chain E from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4har E  26 ACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPV 121
                                    35        45        55        65        75        85        95       105       115      


Chain F from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeeeeee.............hhhhh.......hhhhhhhhhh......eeeee..eeeeeeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4har F  25 EACVTSWLWSEGEGAVFYRVDLHFTNLGTPPLDEDGRWDPALMYNPCGPEPPAHVVRAYNQPAGDVRGVWGKGERTYAEQDFRVGGTRWHRLLRMPVRG 123
                                    34        44        54        64        74        84        94       104       114
   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  (0, 0)

(no "SCOP Domain" information available for 4HAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 24)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4har
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  POLS_RUBVM | P08563
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  Q8QL55_RUBV | Q8QL55
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLS_RUBVM | P08563: 4adg 4adi 4adj 4b3v 4hbe 4hbo 5khc
        Q8QL55_RUBV | Q8QL55: 4hbe 4hbo

(-) Related Entries Specified in the PDB File

4hbe 4hbo