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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  E. COLI BAM COMPLEX (BAMABCDE) BY CRYOEM
 
Authors :  M. G. Iadanza, N. A. Ranson, S. E. Radford, A. J. Higgins, B. Schffrin, A. N. Calabrese, A. E. Ashcroft, D. J. Brockwell
Date :  19 Jul 16  (Deposition) - 12 Oct 16  (Release) - 18 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Membrane Protein, Bam, Omp, Beta Barrel, Outer Membrane, Gram Negative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Iadanza, A. J. Higgins, B. Schiffrin, A. N. Calabrese, D. J. Brockwell, A. E. Ashcroft, S. E. Radford, N. A. Ranson
Lateral Opening In The Intact Beta-Barrel Assembly Machiner Captured By Cryo-Em.
Nat Commun V. 7 12865 2016
PubMed-ID: 27686148  |  Reference-DOI: 10.1038/NCOMMS12865

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BAMB, YFGL, B2512, JW2496
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
 
Molecule 2 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMC
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BAMC, DAPX, NLPB, B2477, JW2462
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
 
Molecule 3 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMD
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BAMD, YFIO, Z3889, ECS3458
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 4 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAME
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BAME, SMPA, C3139
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 5 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BAMA, YAET, ECS88_0187
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5LJO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LJO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LJO)

(-) 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:783
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......hhhhhhhhh........hhhhhhhhhhhhhh...eee..eeee..eeee..ee...eeeeeee.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.hhh.eeeeeeeeeeee.eeeeeeee.....hhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee.....eeeeeeeeee...hhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeee......eeeeeee......hhhhhh..........hhhhhhhhhhhhhhhh.eee....eee.......eeeeee.ee....ee.............eeeeee..hhhhh..eeeeeeee...eeeeeeeeee........eeeeeeeeeee..........eeeeeeeeeeeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh...........eeeeeeeeeeeeeeeeee........eeeeeeeeeee.......eeeeeeeeeeeee.......eeeeeeeeeeeee......hhhhh..........ee..............................................eeeeeeeeeee.....hhhhhh..eeeeeeeeeeee.....................eeeeeeeeeeee..eeeeeeee..........ee.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljo A  24 FVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNI 806
                                    33        43        53        63        73        83        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       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803   


Chain B from PDB  Type:PROTEIN  Length:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.................eeee.................eee..eeeee....eeeeee.....eeeeee...................eee..eeeee....eeeeee.....eeeeee.........eee..eeeee....eeeeee.....eeeeee......ee......eee..eeee.....eeeeee....eeeeeee....................eee..eeeee.....eeeee.....eeeee......eeeee..eeeee.....eeee......eeeee...........eee..eeeee....eeeee......eeeeee.................eee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljo B  22 LFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR 392
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 


Chain C from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh...............................hhhhh.................eee..eee..ee.....hhhhhhhhhhhhhh..eeeee....eeeeeeeeee......eeeeeeeeeeee...eeeeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljo C  25 CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVA 189
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184     


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ljo D  26 EVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS 243
                                    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:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.....hhhhhhhhhh............eeeeeee.......eeeeeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 5ljo E  24 ERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPAL 110
                                    33        43        53        63        73        83        93       103
   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 5LJO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BAMA_ECOLI | P0A940: 2qcz 2qdf 2v9h 3efc 3og5 3q6b 4c4v 4n75 4pk1 4xga 5ayw 5d0o 5d0q 5ekq
        BAMB_ECOLI | P77774: 2yh3 2yms 3p1l 3prw 3q7m 3q7n 3q7o 4pk1 4xga 5ayw 5d0o
        BAMC_ECOLI | P0A903: 2lae 2laf 2yh5 2yh6 3sns 3tgo 5ayw 5d0o 5d0q 5ekq
        BAMD_ECOLI | P0AC02: 2yhc 3q5m 3tgo 5ayw 5d0o 5d0q 5ekq
        BAME_ECOLI | P0A937: 2km7 2kxx 2yh9 5ayw 5d0o 5d0q 5ekq

(-) Related Entries Specified in the PDB File

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