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(-) Description

Title :  CRYSTAL STRUCTURE OF COLICIN E3 IN COMPLEX WITH ITS IMMUNITY PROTEIN
 
Authors :  S. Soelaiman, K. Jakes, N. Wu, C. Li, M. Shoham
Date :  09 Jun 01  (Deposition) - 30 Nov 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Translocation Domain Is A Beta-Jellyroll, The Receptor-Binding Domain Is A Coiled Coil, The Rnase Domain Is A Six-Stranded Antiparallel Beta-Sheet. The Immunity Protein Is A Four-Stranded Antiparallel Beta Sheet Flanked By 3 Helices On One Side Of The Sheet, Ribosome Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Soelaiman, K. Jakes, N. Wu, C. Li, M. Shoham
Crystal Structure Of Colicin E3: Implications For Cell Entr And Ribosome Inactivation.
Mol. Cell V. 8 1053 2001
PubMed-ID: 11741540  |  Reference-DOI: 10.1016/S1097-2765(01)00396-3

(-) Compounds

Molecule 1 - COLICIN E3
    Chains: A, C
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110
    Synonym: RIBONUCLEASE, COLICIN E3 A CHAIN
 
Molecule 2 - COLICIN E3 IMMUNITY PROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110
    Synonym: IMME3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2GOL4Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GOL2Ligand/IonGLYCEROL
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:545 , ASN A:546 , ILE A:547 , LYS A:549 , HOH A:925BINDING SITE FOR RESIDUE CIT A 601
2AC2SOFTWAREGLN A:512 , HIS A:513 , HOH A:922 , HOH A:983 , HOH A:5980BINDING SITE FOR RESIDUE CIT A 602
3AC3SOFTWAREARG C:545 , ASN C:546 , ILE C:547 , LYS C:549 , HOH C:917 , HOH C:5925BINDING SITE FOR RESIDUE CIT C 5601
4AC4SOFTWAREGLN C:512 , HIS C:513 , HOH C:980 , HOH C:5922 , HOH C:5983BINDING SITE FOR RESIDUE CIT C 5602
5AC5SOFTWAREPHE A:378 , VAL C:139 , LEU C:140 , ASP C:187BINDING SITE FOR RESIDUE GOL C 701
6AC6SOFTWARELYS A:458 , GLY B:1 , ASP B:27 , TYR B:79 , ASP B:81 , GLY B:82BINDING SITE FOR RESIDUE GOL B 702
7AC7SOFTWAREVAL A:139 , LEU A:140 , ASP A:187 , PHE C:378BINDING SITE FOR RESIDUE GOL A 5701
8AC8SOFTWARELYS C:458 , GLY D:1 , ASP D:27 , TYR D:79 , ASP D:81 , GLY D:82BINDING SITE FOR RESIDUE GOL D 5702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JCH)

(-) Exons   (0, 0)

(no "Exon" information available for 1JCH)

(-) 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:468
 aligned with CEA3_ECOLX | P00646 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:468
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543        
           CEA3_ECOLX    84 VAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL 551
               SCOP domains d1jcha2 A:84-315 Colicin E3 N-terminal domain                                                                                                                                                                                           d1jcha3 A:316-454 Colicin E3 receptor domain                                                                                               d1jcha1 A:455-551 Ribonuclease domain of colicin E3                                               SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1jchA02 A:293-453 Helix Hairpins                                                                                                                                 1jchA03 A:454-551 Ribonuclease domain of colicin e3 (Residues 456-551)                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............................hhhhhhhhhhh......eee...................ee...............eee........ee....ee...........eee.................................................eee.............ee............eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhh................eee..............eee.....eeee.........eee.....eeeee......eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jch A  84 VAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAFGTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL 551
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543        


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with IMM3_ECOLX | P02984 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
           IMM3_ECOLX     2 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  85
               SCOP domains d1jchb_ B: Colicin E3 immunity protein                                               SCOP domains
               CATH domains 1jchB00 B:1-84  [code=3.10.50.20, no name defined]                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeeeee.......hhhhhhhh...........ee.hhhhhhhhhhhh........eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1jch B   1 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  84
                                    10        20        30        40        50        60        70        80    


Chain C from PDB  Type:PROTEIN  Length:468
 aligned with CEA3_ECOLX | P00646 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:468
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543        
           CEA3_ECOLX    84 VAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL 551
               SCOP domains d1jchc2 C:84-315 Colicin E3 N-terminal domain                                                                                                                                                                                           d1jchc3 C:316-454 Colicin E3 receptor domain                                                                                               d1jchc1 C:455-551 Ribonuclease domain of colicin E3                                               SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1jchC02 C:293-453 Helix Hairpins                                                                                                                                 1jchC03 C:454-551 Ribonuclease domain of colicin e3 (Residues 456-551)                             CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------Pyocin_S-1jchC01 C:171-286                                                                                          ---------------------------E2R135-1jchC05 C:314-447                                                                                                              ----------------Cytotoxic-1jchC03 C:464-551                                                              Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------Pyocin_S-1jchC02 C:171-286                                                                                          ---------------------------E2R135-1jchC06 C:314-447                                                                                                              ----------------Cytotoxic-1jchC04 C:464-551                                                              Pfam domains (2)
         Sec.struct. author ...............................hhhhhhhhhhh......eee...................ee...............eee........ee....ee...........eee.................................................eee.............ee............eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhh................eee..............eee.....eeee.........eee.....eeeee......eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jch C  84 VAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAFGTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL 551
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543        


Chain D from PDB  Type:PROTEIN  Length:84
 aligned with IMM3_ECOLX | P02984 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
           IMM3_ECOLX     2 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  85
               SCOP domains d1jchd_ D: Colicin E3 immunity protein                                               SCOP domains
               CATH domains 1jchD00 D:1-84  [code=3.10.50.20, no name defined]                                   CATH domains
           Pfam domains (1) Cloacin_immun-1jchD01 D:1-82                                                      -- Pfam domains (1)
           Pfam domains (2) Cloacin_immun-1jchD02 D:1-82                                                      -- Pfam domains (2)
         Sec.struct. author .eeeeeeeee.....eeeeee.......hhhhhhhh...........ee.hhhhhhhhhhhh........eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1jch D   1 GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW  84
                                    10        20        30        40        50        60        70        80
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (4, 8)

Asymmetric Unit
(-)
Clan: Bacteriocin_TLN (3)
(-)
Clan: no clan defined [family: Cloacin_immun] (1)
(-)
Clan: no clan defined [family: Cytotoxic] (1)
(-)
Clan: no clan defined [family: E2R135] (3)

(-) Gene Ontology  (14, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (CEA3_ECOLX | P00646)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

Chain B,D   (IMM3_ECOLX | P02984)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
    GO:0030153    bacteriocin immunity    A process that mediates resistance to a bacteriocin: any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary.

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  IMM3_ECOLX | P02984
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA3_ECOLX | P00646: 1e44 1ujw 2b5u 4udm 4v5k
        IMM3_ECOLX | P02984: 1e44 2b5u 3eip 4udm

(-) Related Entries Specified in the PDB File

1e44 CRYSTAL STRUCTURE OF A FRAGMENT COORESPONDING TO THE C DOMAIN IN COMPLEX WITH THE IMMUNITY PROTEIN
3eip CRYSTAL STRUCTURE OF FREE IMMUNITY PROTEIN TO COLICIN E3