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(-) Description

Title :  CRYSTAL STRUCTURE OF W-W-R CLPX HEXAMER
 
Authors :  S. E. Glynn, A. R. Nager, B. S. Stinson, K. R. Schmitz, T. A. Baker, R. T. Sa
Date :  28 Nov 12  (Deposition) - 15 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.48
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Atpase, Hexameric, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Stinson, A. R. Nager, S. E. Glynn, K. R. Schmitz, T. A. Baker, R. T. Sauer
Nucleotide Binding And Conformational Switching In The Hexameric Ring Of A Aaa+ Machine.
Cell(Cambridge, Mass. ) V. 153 628 2013
PubMed-ID: 23622246  |  Reference-DOI: 10.1016/J.CELL.2013.03.029

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC
    Expression System Strain: BLR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B0438, CLPX, JW0428, LOPC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:122 , SER A:123 , GLY A:124 , LYS A:125 , THR A:126BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREPRO B:120 , GLY B:122 , SER B:123 , GLY B:124 , LYS B:125 , THR B:126BINDING SITE FOR RESIDUE SO4 B 501
3AC3SOFTWAREPRO C:120 , THR C:121 , GLY C:122 , SER C:123 , GLY C:124 , LYS C:125 , THR C:126 , TYR C:182BINDING SITE FOR RESIDUE SO4 C 501
4AC4SOFTWAREGLY D:122 , SER D:123 , GLY D:124 , LYS D:125 , THR D:126BINDING SITE FOR RESIDUE SO4 D 501
5AC5SOFTWAREGLY E:122 , SER E:123 , GLY E:124 , LYS E:125 , THR E:126BINDING SITE FOR RESIDUE SO4 E 501
6AC6SOFTWAREPRO F:120 , GLY F:122 , SER F:123 , GLY F:124 , LYS F:125 , THR F:126BINDING SITE FOR RESIDUE SO4 F 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I5O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I5O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I5O)

(-) Exons   (0, 0)

(no "Exon" information available for 4I5O)

(-) Sequences/Alignments

Asymmetric/Biological 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:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhh...hhhhhhh.eeeeehhhhh.....hhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh....hhhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5o A  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKSRDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETGSASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102   ||  115       125       135       145  ||   158       168       178       188    || 204       214   ||  240       250       260     ||284       294       304       314       324       334       344       354       364       374       384       394       404         
                                                                     106|                                   148|                                      193|               218|                            266|                                                                                                                                    
                                                                      110                                    152                                       200                235                             281                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhh...hhhhhhh.eeeeehhhhh.....hhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh....hhhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhh.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5o B  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKSRDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETGSASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102|      119       129       139       149       159       169       179       189   ||  205       215  ||   241       251       261    || 285       295       305       315       325       335       345       355       365       375       385       395       405        
                                                                 102|                                                                                193|               218|                            266|                                                                                                                                    
                                                                  110                                                                                 200                235                             281                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............eeee.....hhhhhhhhhhhhh...eeeee.......hhhhh..hhhhhhhhhh...hhhhhhh.eeeeehhhhh........hhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh....hhhhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeehhhhhh......eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5o C  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKSDNPRDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETGSASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLI 412
                                    72        82        92       102       112       122       132       142       152       162       172       182       192   ||  205       215  ||   241       251       261    || 285       295       305       315       325       335       345       355       365       375       385       395       405       
                                                                                                                                                               196|               218|                            266|                                                                                                                                   
                                                                                                                                                                200                235                             281                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhh...eeeee..............hhhhhhhhhh...hhhhhhh.eeeeehhhhh...hhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh..hhhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5o D  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102||     118       128       138       148       158       168       178       188  ||   207       217||     243       253       263||     289       299       309       319       329       339       349       359       369       379       389       399       409    
                                                                  103|                                                                              191|              218|                          264|                                                                                                                                    
                                                                   110                                                                               201               235                           281                                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............eeee.....hhhhhhhhhhhhh...eeeee.hhh.....hhhhhhhhhhhhhhhh..hhhhhhh.eeeeehhhhh........hhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh....hhhhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i5o E  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKSDNPRDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETGSASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102       112       122       132       142       152       162       172       182       192   ||  205       215  ||   241       251       261    || 285       295       305       315       325       335       345       355       365       375       385       395       405        
                                                                                                                                                               196|               218|                            266|                                                                                                                                    
                                                                                                                                                                200                235                             281                                                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............eeee.....hhhhhhhhhhhhh...eeeee............hhhhhhhhhh...hhhhhhh.eeeeehhhhh....hhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhh...hhhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5o F  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDEIDKISRKDVSGEGVQQALLKLIEGTFLQVDTSKILFICGGAFAGLDKVISHRVETGASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102       112       122       132       142     ||154       164       174       184       202       212     ||238       248       258      |283       293       303       313       323       333       343       353       363       373       383       393       403       413
                                                                                                               148|                                      192|              218|                           265|                                                                                                                                    
                                                                                                                151                                       201               235                            281
   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 4I5O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I5O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I5O)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  CLPX_ECOLI | P0A6H1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPX_ECOLI | P0A6H1: 1ovx 2ds5 2ds6 2ds7 2ds8 3hte 3hws 4i34 4i4l 4i63 4i81 4i9k

(-) Related Entries Specified in the PDB File

3hte CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE HEXAMERIC CLPX
3hws CRYSTAL STRUCTURE OF NUCLEOTIDE-BOUND HEXAMERIC CLPX
4i34 CRYSTAL STRUCTURE OF W-W-W CLPX HEXAMER
4i4l CRYSTAL STRUCTURE OF NUCLEOTIDE-BOUND W-W-W CLPX HEXAMER
4i63 CRYSTAL STRUCTURE OF E-R CLPX HEXAMER