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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF MU PHAGE CENTRAL SPIKE
 
Authors :  K. Harada, E. Yamashita, A. Nakagawa, S. Takeda
Date :  01 Jun 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym. Unit :  A,B,C,P,Q,R
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  P,Q,R  (1x)
Keywords :  Beta-Helix, Central Spike, Mu Phage, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Harada, E. Yamashita, A. Nakagawa, T. Miyafusa, K. Tsumoto, T. Ueno Y. Toyama, S. Takeda
Crystal Structure Of The C-Terminal Domain Of Mu Phage Central Spike And Functions Of Bound Calcium Ion
Biochim. Biophys. Acta V. 1834 284 2013
PubMed-ID: 22922659  |  Reference-DOI: 10.1016/J.BBAPAP.2012.08.015

(-) Compounds

Molecule 1 - PROTEIN GP45
    Chains: A, B, C, P, Q, R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 92-197
    Gene: 45
    Organism Scientific: ENTEROBACTERIA PHAGE MU
    Organism Taxid: 10677

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCPQR
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    PQR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:183 , HIS A:185 , HIS B:183 , HIS B:185 , HIS C:183 , HIS C:185BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREASP A:188 , SER A:189 , ASP B:188 , SER B:189 , ASP C:188 , SER C:189BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREGLY A:187 , ASP A:188 , GLY B:187 , ASP B:188 , GLY C:187 , ASP C:188BINDING SITE FOR RESIDUE CL C 301
4AC4SOFTWAREHIS P:183 , HIS P:185 , HIS Q:183 , HIS Q:185 , HIS R:183 , HIS R:185BINDING SITE FOR RESIDUE FE P 301
5AC5SOFTWAREGLY P:187 , ASP P:188 , GLY Q:187 , ASP Q:188 , GLY R:187 , ASP R:188BINDING SITE FOR RESIDUE CL P 302
6AC6SOFTWAREASP P:188 , SER P:189 , ASP Q:188 , SER Q:189 , ASP R:188 , SER R:189BINDING SITE FOR RESIDUE CA Q 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VTO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VTO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VTO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VTO)

(-) Exons   (0, 0)

(no "Exon" information available for 3VTO)

(-) 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:99
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:99
                                                                                                                         197   
                                   111       121       131       141       151       161       171       181       191     |   
            BP45_BPMU   102 GDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ---   -
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3vto A 102 GDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQLEH 200
                                   111       121       131       141       151       161       171       181       191         


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:110
                                                                                                                                    197   
                                   100       110       120       130       140       150       160       170       180       190      |  -
            BP45_BPMU    91 DRRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ---   -
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3vto B  91 MRRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQLEH 200
                                   100       110       120       130       140       150       160       170       180       190       200


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:109
                                                                                                                                   197   
                                   101       111       121       131       141       151       161       171       181       191     |   
            BP45_BPMU    92 RRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3vto C  92 RRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQLEH 200
                                   101       111       121       131       141       151       161       171       181       191         


Chain P from PDB  Type:PROTEIN  Length:103
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:103
                                                                                                                            197    
                                   108       118       128       138       148       158       168       178       188        |-   
            BP45_BPMU    99 LEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ----   -
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3vto P  99 LEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQLEHH 201
                                   108       118       128       138       148       158       168       178       188       198   


Chain Q from PDB  Type:PROTEIN  Length:108
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:108
                                                                                                                                    197 
                                   100       110       120       130       140       150       160       170       180       190      | 
            BP45_BPMU    91 DRRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............................................................................................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3vto Q  91 MRRYRPTNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQL 198
                                   100       110       120       130       140       150       160       170       180       190        


Chain R from PDB  Type:PROTEIN  Length:103
 aligned with BP45_BPMU | Q9T1V4 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:103
                                                                                                                              197  
                                   106       116       126       136       146       156       166       176       186       196|  
            BP45_BPMU    97 TNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQ--   -
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3vto R  97 TNLEPGDAGIYHHEGHRIRLTKDGRCIITCKTVEVYADESMTVDTPRTTFTGDVEIQKGLGVKGKSQFDSNITAPDAIINGKSTDKHIHRGDSGGTTGPMQLE 199
                                   106       116       126       136       146       156       166       176       186       196
   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 3VTO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VTO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VTO)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,P,Q,R   (BP45_BPMU | Q9T1V4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BP45_BPMU | Q9T1V4: 3vtn

(-) Related Entries Specified in the PDB File

3vtn