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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LEGIONELLA PNEUMOPHILA EFFECTOR PROTEIN RAVZ - F222
 
Authors :  D. H. Kwon, L. -H. Kim, B. -W. Kim, S. B. Hong, H. K. Song
Date :  26 Mar 16  (Deposition) - 09 Nov 16  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (2x)
Biol. Unit 4:  B  (2x)
Keywords :  Autophagy, Atg8, Deconjugating Enzyme, Protease, Atg4B, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Kwon, S. Kim, Y. O. Jung, K. H. Roh, L. Kim, B. -W. Kim, S. B. Hong, I. Y. Lee, J. H. Song, W. C. Lee, E. J. Choi, K. Y. Hwang, H. K. Song
The 1:2 Complex Between Ravz And Lc3 Reveals A Mechanism Fo Deconjugation Of Lc3 On The Phagophore Membrane
Autophagy V. 13 70 2017
PubMed-ID: 27791457  |  Reference-DOI: 10.1080/15548627.2016.1243199

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN RAVZ
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LPG1683
    Mutation: YES
    Organism Scientific: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STRAIN PHILADELPHIA 1
    Organism Taxid: 272624
    Strain: PHILADELPHIA 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): A 
Biological Unit 4 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5IZV)

(-) Sites  (0, 0)

(no "Site" information available for 5IZV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (17, 17)

Asymmetric Unit
No.Residues
1Glu A:92 -Asp A:93
2Asp A:93 -Lys A:94
3Ser A:188 -Lys A:189
4Arg A:201 -Asp A:202
5Glu A:255 -Gly A:256
6Gln A:346 -Ser A:347
7Gly A:378 -Lys A:379
8Lys A:379 -Asn A:380
9Asp A:429 -Asp A:430
10Glu B:92 -Asp B:93
11Asp B:93 -Lys B:94
12Ser B:188 -Lys B:189
13Glu B:255 -Gly B:256
14Gln B:346 -Ser B:347
15Gly B:378 -Lys B:379
16Lys B:379 -Asn B:380
17Asp B:429 -Asp B:430

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IZV)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhh.hhhhhhhhhhhhhh..........eee........eeeeee.....eeeee......eeee........eeehhhhhhhhhhhhhhhhhh...eeeeeeeeeee........eeeeeeeeee....eeeeeeee.....hhhhh...hhhhh....hhhhhhhhhhhhh.....ee...eeee..........hhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhh......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izv A  49 SIYPPETSWEVNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDSDYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQVLLTISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFTLGKFTRAAYNHQNRLTEGNSGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHVQDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEIGYSKTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESLQKLVLPCVKFDD 430
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348|      364       374       384       394       404       414       424      
                                                                                                                                                                                                                                                                                                                                     348|                                                                           
                                                                                                                                                                                                                                                                                                                                      355                                                                           


Chain B from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......hhhhh.hhhhhhhhhhhhhh..........eee........eeeeee.....eeeee......eeee........eeehhhhhhhhhhhhhhhhh....eeeeeeeeeee........eeeeeeeeee....eeeeeeee......hhhhh....hhhhhhhhhhhhh.....ee...eeee..........hhhhhhhhhhhhhhhhhhh.....ee..ee.hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izv B  49 SIYPPETSWEVNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDSDYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQVLLTISYDPKSKQLTPTVYDSISLSSYFKGKYRTTCDEILTQSIEKAIKSTDFTLGKFTRAAYNHQNRLTEGNSGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHVQDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEIGYSKTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESLQKLVLPCVKFDD 430
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198||     215       225       235       245       255       265       275       285       295       305       315       325       335       345  ||   361       371       381       391       401       411       421         
                                                                                                                                                                                199|                                                                                                                                          348|                                                                           
                                                                                                                                                                                 207                                                                                                                                           355
   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 5IZV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5IZV)

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  Cis Peptide Bonds
    Arg A:201 - Asp A:202   [ RasMol ]  
    Asp A:429 - Asp A:430   [ RasMol ]  
    Asp A:93 - Lys A:94   [ RasMol ]  
    Asp B:429 - Asp B:430   [ RasMol ]  
    Asp B:93 - Lys B:94   [ RasMol ]  
    Gln A:346 - Ser A:347   [ RasMol ]  
    Gln B:346 - Ser B:347   [ RasMol ]  
    Glu A:255 - Gly A:256   [ RasMol ]  
    Glu A:92 - Asp A:93   [ RasMol ]  
    Glu B:255 - Gly B:256   [ RasMol ]  
    Glu B:92 - Asp B:93   [ RasMol ]  
    Gly A:378 - Lys A:379   [ RasMol ]  
    Gly B:378 - Lys B:379   [ RasMol ]  
    Lys A:379 - Asn A:380   [ RasMol ]  
    Lys B:379 - Asn B:380   [ RasMol ]  
    Ser A:188 - Lys A:189   [ RasMol ]  
    Ser B:188 - Lys B:189   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        Q5ZUV9_LEGPH | Q5ZUV9: 5cqc 5hzy 5io3 5ms2 5ms5 5ms7 5ms8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IZV)