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(-) Description

Title :  C1882 PAAR-REPEAT PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH A VGRG-LIKE BETA-HELIX THAT IS BASED ON A FRAGMENT OF T4 GP5
 
Authors :  S. A. Buth, P. G. Leiman, M. M. Shneider
Date :  07 Mar 13  (Deposition) - 14 Aug 13  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Biol. Unit 4:  M,N,O,P  (1x)
Keywords :  Paar-Repeat Motif, Membrane Piercing, Type Vi Secretion System, T6Ss Spike, Cell Puncturing Device, Beta-Helix, T4 Gp5, Vgrg Tip, Cft073, Vgrg Protein, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Shneider, S. A. Buth, B. T. Ho, M. Basler, J. J. Mekalanos, P. G. Leiman
Paar-Repeat Proteins Sharpen And Diversify The Type Vi Secretion System Spike.
Nature V. 500 350 2013
PubMed-ID: 23925114  |  Reference-DOI: 10.1038/NATURE12453

(-) Compounds

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
    Chains: A, B, C, E, F, G, I, J, K, M, N, O
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEEVA2, PET-23A DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GP5G484, UNP RESIDUES 484-575
    Gene: 5
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: PROTEIN GP5, GP5*, GP5C
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: D, H, L, P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEEVA2, PET-23A DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C1882
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 199310
    Strain: CFT073
    Synonym: C1882

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit : ABCDEFGHIJKLMNOP
Biological Unit 1 (1x): ABCD            
Biological Unit 2 (1x):     EFGH        
Biological Unit 3 (1x):         IJKL    
Biological Unit 4 (1x):             MNOP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG4Ligand/IonMAGNESIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:601 , HOH A:602 , HOH B:701 , HOH B:702 , GLU C:552 , HOH C:601 , HOH C:602BINDING SITE FOR RESIDUE MG B 601
02AC2SOFTWAREHIS D:14 , HIS D:46 , HIS D:54 , CYS D:81BINDING SITE FOR RESIDUE ZN D 101
03AC3SOFTWARELYS E:488 , LYS F:488 , LYS G:488BINDING SITE FOR RESIDUE CL E 601
04AC4SOFTWAREHOH E:701 , HOH E:702 , HOH F:701 , HOH F:702 , HOH G:601 , HOH G:602BINDING SITE FOR RESIDUE MG F 601
05AC5SOFTWAREHIS H:14 , HIS H:46 , HIS H:54 , CYS H:81BINDING SITE FOR RESIDUE ZN H 101
06AC6SOFTWAREHOH I:701 , HOH I:702 , HOH J:601 , HOH J:602 , HOH K:601 , HOH K:602BINDING SITE FOR RESIDUE MG I 601
07AC7SOFTWAREHIS L:14 , HIS L:46 , HIS L:54 , CYS L:81BINDING SITE FOR RESIDUE ZN L 101
08AC8SOFTWARELYS M:488 , LYS N:488BINDING SITE FOR RESIDUE CL M 601
09AC9SOFTWAREHOH M:701 , HOH N:601 , HOH N:602 , GLU O:552 , HOH O:701 , HOH O:702 , HOH O:703BINDING SITE FOR RESIDUE MG O 601
10BC1SOFTWAREHIS P:14 , HIS P:46 , HIS P:54 , CYS P:81BINDING SITE FOR RESIDUE ZN P 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JIW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JIW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JIW)

(-) 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:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eeeee...eeeee...eeee....eeeee....eeee...eeeee...eeeee..eeeeee.eeeeee..eeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw A 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain B from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeee...eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw B 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw C 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........ee.......eee..ee......eeeee.......eeee.......eee..ee.............ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw D   2 PLAAKLTDKGTQHDGYYETVITAGSSTVFIDGLPAARQEDPLTPHDKPKHPPHPRKIARGSSTVFIDGLPAARTGDAIDCGGVVIGGGTVNIG  94
                                    11        21        31        41        51        61        71        81        91   


Chain E from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee..eeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw E 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw F 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain G from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeee....eeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw G 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain H from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........ee.......eee..ee......eeeeeee..eeeeeee.......eee..ee.............ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw H   2 PLAAKLTDKGTQHDGYYETVITAGSSTVFIDGLPAARQEDPLTPHDKPKHPPHPRKIARGSSTVFIDGLPAARTGDAIDCGGVVIGGGTVNIG  94
                                    11        21        31        41        51        61        71        81        91   


Chain I from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw I 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain J from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw J 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain K from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw K 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain L from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........ee.......eee..ee......eeeee.......eeee.......eee..ee...................eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw L   2 PLAAKLTDKGTQHDGYYETVITAGSSTVFIDGLPAARQEDPLTPHDKPKHPPHPRKIARGSSTVFIDGLPAARTGDAIDCGGVVIGGGTVNIG  94
                                    11        21        31        41        51        61        71        81        91   


Chain M from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeee...eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw M 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain N from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw N 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain O from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee..eeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw O 483 SGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLN 575
                                   492       502       512       522       532       542       552       562       572   


Chain P from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........ee.......eee..ee......eeeee.......eeee.......eee..ee...................eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4jiw P   2 PLAAKLTDKGTQHDGYYETVITAGSSTVFIDGLPAARQEDPLTPHDKPKHPPHPRKIARGSSTVFIDGLPAARTGDAIDCGGVVIGGGTVNIG  94
                                    11        21        31        41        51        61        71        81        91
   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 4JIW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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  BP5_BPT4 | P16009
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 Related Entries

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

UniProtKB/Swiss-Prot
        BP5_BPT4 | P16009: 1k28 1pdl 1wth 2z6b 3a1m 4jiv 4jj2 4ku0 4osd 5iv5

(-) Related Entries Specified in the PDB File

1k28 THE STRUCTURE OF THE FULL LENGTH GP5 PROTEIN FROM PHAGE T4
4jiv