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(-) Description

Title :  THE STRUCTURE OF THE BAMACDE SUBCOMPLEX FROM E. COLI
 
Authors :  J. Bakelar, S. K. Buchanan, N. Noinaj
Date :  04 Nov 15  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym./Biol. Unit :  A,C,D,E
Keywords :  Membrane Protein, Insertase, Beta-Barrel, Outer Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bakelar, S. K. Buchanan, N. Noinaj
The Structure Of The Beta-Barrel Assembly Machinery Complex
Science V. 351 180 2016
PubMed-ID: 26744406  |  Reference-DOI: 10.1126/SCIENCE.AAD3460

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 21-810
    GeneBAMA, YAET, YZZN, YZZY, B0177, JW0172
    Organism ScientificESCHERICHIA COLI (STRAIN K12)
    Organism Taxid83333
    StrainK12
    SynonymOMP85
 
Molecule 2 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMD
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 20-245
    GeneBAMD, YFIO, B2595, JW2577
    Organism ScientificESCHERICHIA COLI (STRAIN K12)
    Organism Taxid83333
    StrainK12
 
Molecule 3 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMC
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 25-344
    GeneBAMC, DAPX, NLPB, B2477, JW2462
    Organism ScientificESCHERICHIA COLI (STRAIN K12)
    Organism Taxid83333
    StrainK12
 
Molecule 4 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAME
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 20-113
    GeneBAME, SMPA, B2617, JW2598
    Organism ScientificESCHERICHIA COLI (STRAIN K12)
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ACDE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5EKQ)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:690 -A:700

(-) Cis Peptide Bonds  (42, 42)

Asymmetric/Biological Unit
No.Residues
1Glu A:32 -Gly A:33
2Gly A:51 -Asp A:52
3Gly A:81 -Asp A:82
4Ser A:117 -Gly A:118
5Glu A:123 -Ser A:124
6Gly A:172 -Val A:173
7Val A:183 -Gly A:184
8Ala A:187 -Phe A:188
9Ser A:195 -His A:196
10Gln A:198 -Leu A:199
11Asp A:201 -Glu A:202
12Pro A:204 -Trp A:205
13Trp A:205 -Trp A:206
14Gly A:210 -Asp A:211
15Ile A:260 -Thr A:261
16Asn A:276 -Leu A:277
17Gly A:279 -His A:280
18Glu A:396 -Thr A:397
19Ala A:499 -Asp A:500
20Pro A:602 -Gly A:603
21Lys A:644 -Glu A:645
22Gln A:693 -Asp A:694
23Asp A:750 -Ser A:751
24Gln A:789 -Pro A:790
25Lys A:793 -Tyr A:794
26Ile A:806 -Gly A:807
27Gly A:807 -Lys A:808
28Gly D:65 -Pro D:66
29Thr D:101 -His D:102
30His D:102 -Pro D:103
31Pro D:103 -Asn D:104
32Ser D:122 -Ala D:123
33Gln D:125 -Gly D:126
34Arg D:152 -Gly D:153
35Ser D:243 -Asn D:244
36Val C:60 -Thr C:61
37Gly C:63 -Asp C:64
38Gly C:72 -Ser C:73
39Pro C:88 -Leu C:89
40Gly C:101 -Asp C:102
41Val E:27 -Tyr E:28
42Pro E:67 -Phe E:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EKQ)

(-) 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:763
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh............hhhhhhhhhhhhhh.eeeeeeee....eeeeeee......eee.....hhhhhh.......hhhhhhhhhhhhhhhh.........eeee.....eeeee............eee......hhhhhh.......................hhhhhhhhhhhhhhhh.......eeeeeee......eeeeee...........eeeee.....hhhhhhhh........hhhhhhhhhhhhhhhhhhh......eeeeeee......eeeeeee......eeeeeeee.....hhhhhhhh......ee....hhhhhhhhhhhhh....eeeeeeee..eeeeeeeeeee......eeeee..eeeeeee........eeeeeeee...eeeeeeeeee........eeeeeeeeeeee.........eeeeeeeeeeeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh...........eeeeeeeeeeeeeeeeee........eeeeeeeeeee.......eeeeeeeeeeeee.......eeeeeeeeeeeee................................ee.........................ee........eeeeeeeeeee........hhh.eeeeeeeeeeeee.....................eeeeeeeeeee....eeeeeee..............eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ekq A  29 IHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGISFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW 810
                                    38        48        58        68        78        88        98 ||    116       126       136       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429||     447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807   
                                                                                                 100|                                144|                                                                                                                                                                                                                                                                                       430|                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                  109                                 148                                                                                                                                                                                                                                                                                        439                                                                                                                                                                                                                                                                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh...............................hhhhh...............................hhhhhhhhhh...eeeee....eeee.................eeeee.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ekq C  27 SDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALGARTQFTGDTASLGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSAT 214
                                    36        46        56        66        76        86    ||  98       112       122       132       142       152       162    || 175       185       195       205         
                                                                                           91|         106|                                                     167|                                           
                                                                                            94          111                                                      171                                           

Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ekq D  26 EVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSN 244
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235         

Chain E from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee......hhhhh.................ee......eeeeeeeee......eeeeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5ekq E  22 TLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALS 111
                                    31        41        51        61        71        81        91       101       111

   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 5EKQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
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  Cis Peptide Bonds
    Ala A:187 - Phe A:188   [ RasMol ]  
    Ala A:499 - Asp A:500   [ RasMol ]  
    Arg D:152 - Gly D:153   [ RasMol ]  
    Asn A:276 - Leu A:277   [ RasMol ]  
    Asp A:201 - Glu A:202   [ RasMol ]  
    Asp A:750 - Ser A:751   [ RasMol ]  
    Gln A:198 - Leu A:199   [ RasMol ]  
    Gln A:693 - Asp A:694   [ RasMol ]  
    Gln A:789 - Pro A:790   [ RasMol ]  
    Gln D:125 - Gly D:126   [ RasMol ]  
    Glu A:123 - Ser A:124   [ RasMol ]  
    Glu A:32 - Gly A:33   [ RasMol ]  
    Glu A:396 - Thr A:397   [ RasMol ]  
    Gly A:172 - Val A:173   [ RasMol ]  
    Gly A:210 - Asp A:211   [ RasMol ]  
    Gly A:279 - His A:280   [ RasMol ]  
    Gly A:51 - Asp A:52   [ RasMol ]  
    Gly A:807 - Lys A:808   [ RasMol ]  
    Gly A:81 - Asp A:82   [ RasMol ]  
    Gly C:101 - Asp C:102   [ RasMol ]  
    Gly C:63 - Asp C:64   [ RasMol ]  
    Gly C:72 - Ser C:73   [ RasMol ]  
    Gly D:65 - Pro D:66   [ RasMol ]  
    His D:102 - Pro D:103   [ RasMol ]  
    Ile A:260 - Thr A:261   [ RasMol ]  
    Ile A:806 - Gly A:807   [ RasMol ]  
    Lys A:644 - Glu A:645   [ RasMol ]  
    Lys A:793 - Tyr A:794   [ RasMol ]  
    Pro A:204 - Trp A:205   [ RasMol ]  
    Pro A:602 - Gly A:603   [ RasMol ]  
    Pro C:88 - Leu C:89   [ RasMol ]  
    Pro D:103 - Asn D:104   [ RasMol ]  
    Pro E:67 - Phe E:68   [ RasMol ]  
    Ser A:117 - Gly A:118   [ RasMol ]  
    Ser A:195 - His A:196   [ RasMol ]  
    Ser D:122 - Ala D:123   [ RasMol ]  
    Ser D:243 - Asn D:244   [ RasMol ]  
    Thr D:101 - His D:102   [ RasMol ]  
    Trp A:205 - Trp A:206   [ RasMol ]  
    Val A:183 - Gly A:184   [ RasMol ]  
    Val C:60 - Thr C:61   [ RasMol ]  
    Val E:27 - Tyr E:28   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAMA_ECOLI | P0A9402qcz 2qdf 2v9h 3efc 3og5 3q6b 4c4v 4n75 4pk1 4xga 5ayw 5d0o 5d0q 5ljo
        BAMC_ECOLI | P0A9032lae 2laf 2yh5 2yh6 3sns 3tgo 5ayw 5d0o 5d0q 5ljo
        BAMD_ECOLI | P0AC022yhc 3q5m 3tgo 5ayw 5d0o 5d0q 5ljo
        BAME_ECOLI | P0A9372km7 2kxx 2yh9 5ayw 5d0o 5d0q 5ljo

(-) Related Entries Specified in the PDB File

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