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(-) Description

Title :  STRUCTURE OF A MEMBRANE COMPLEX
 
Authors :  Y. Huang, L. Han, J. Zheng
Date :  14 Sep 15  (Deposition) - 24 Feb 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.56
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Membrane Protein, Complex, Membrane Biogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Han, J. Zheng, Y. Wang, X. Yang, Y. Liu, C. Sun, B. Cao, H. Zhou, D. Ni, J. Lou, Y. Zhao, Y. Huang
Structure Of The Bam Complex And Its Implications For Biogenesis Of Outer-Membrane Proteins
Nat. Struct. Mol. Biol. V. 23 192 2016
PubMed-ID: 26900875  |  Reference-DOI: 10.1038/NSMB.3181

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-810
    Gene: BAMA, YAET, YZZN, YZZY, B0177, JW0172
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: OMP85
 
Molecule 2 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMB
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 20-392
    Gene: BAMB, YFGL, B2512, JW2496
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
 
Molecule 3 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMC
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 33-88
    Gene: BAMC, DAPX, NLPB, B2477, JW2462
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
 
Molecule 4 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMD
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 20-245
    Gene: BAMD, YFIO, B2595, JW2577
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
 
Molecule 5 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAME
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 20-113
    Gene: BAME, SMPA, B2617, JW2598
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12

 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 5AYW)

(-) Sites  (0, 0)

(no "Site" information available for 5AYW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Gly A:23 -Phe A:24
2Val A:173 -Ser A:174
3Phe A:197 -Gln A:198
4Gln A:198 -Leu A:199
5Leu A:219 -Ala A:220
6Pro A:292 -Gly A:293
7Trp A:449 -Leu A:450
8Asn A:681 -Tyr A:682
9Gly B:114 -Val B:115
10Gly B:196 -Glu B:197
11Gly B:237 -Ser B:238
12Val B:286 -Asn B:287
13Gly C:72 -Ser C:73
14Gln C:87 -Pro C:88
15Gly E:60 -Thr E:61
16Pro E:67 -Phe E:68
17Glu E:84 -Gly E:85
18Gly E:85 -Val E:86
19Ala E:109 -Leu E:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AYW)

(-) 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:785
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhh.........hhhhhhhhhhhhhh...eeeeeeee...eeeeeeee..eeeeeeee.....hhhhhhhhhhh............hhhhhhhhhhhhhhhh.......eeeeee....eeeeeee.......eeeeeeee.....hhhhhh.........................hhhhhhhhhhh......eeeeeeeee.....eeeeeeeee.....eeeeeeeeee...hhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeee.....eeeeeeee.....hhhhhhh..........hhhhhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeeee...eeeeeeee.......eeeeeeee........eeeeeeee...eeeeeeeeee........eeee.eeeeee.hhhhh....eeeeeeee.eeee.....eeeeee.eeeeeeee....hhhhhhhhhhhh..........eeeeeeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeeeee.......eeeeeeeeeeeee......hhhhh..........ee.......eeee.........................eeeeee....eeeeeeeeeeee............eeeee..eeeee.....................eeeeeeeeeeee..eeeeeeeeeeee......ee.ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayw A  22 EGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK 808
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    || 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     
                                                                                                                                                                                                                  206|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                   209                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeee...............eee..eeeee....eeeeee.....eeeeee.........eeeeeeee..eeeeee...eeeeee.....eeeeee.........eee..eeeee....eeeeee.....eeeeee......ee......eee..eeee.....eeeeee.....eeeeee............ee...eeeee.....eeeee.....eeeee........eee..eeeee.....eeeee.....eeeee...........eee..eeeee....eeeeee.....eeeeee.................eee.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ayw B  31 KMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTETTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSIT 391
                                    40        50        60        70        80        90       100|      115       125       135       145       155       165       175       185       195       205       215       225       235    || 253       263       273       283       293       303       313       323       333       343       353       363       373       383        
                                                                                               100|                                                                                                                                   240|                                                                                                                                              
                                                                                                106                                                                                                                                    249                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...............................hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 5ayw C  33 RQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQP  88
                                    42        52        62        72        82      


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayw D  22 GSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS 243
                                    31        41        51        61        71        81        91       101       111       121||     141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                              122|                                                                                                              
                                                                                                                               133                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhh....ee......eeeeeeee.......eeeeeeee........eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5ayw E  24 ERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALS 111
                                    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 5AYW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 41)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala E:109 - Leu E:110   [ RasMol ]  
    Asn A:681 - Tyr A:682   [ RasMol ]  
    Gln A:198 - Leu A:199   [ RasMol ]  
    Gln C:87 - Pro C:88   [ RasMol ]  
    Glu E:84 - Gly E:85   [ RasMol ]  
    Gly A:23 - Phe A:24   [ RasMol ]  
    Gly B:114 - Val B:115   [ RasMol ]  
    Gly B:196 - Glu B:197   [ RasMol ]  
    Gly B:237 - Ser B:238   [ RasMol ]  
    Gly C:72 - Ser C:73   [ RasMol ]  
    Gly E:60 - Thr E:61   [ RasMol ]  
    Gly E:85 - Val E:86   [ RasMol ]  
    Leu A:219 - Ala A:220   [ RasMol ]  
    Phe A:197 - Gln A:198   [ RasMol ]  
    Pro A:292 - Gly A:293   [ RasMol ]  
    Pro E:67 - Phe E:68   [ RasMol ]  
    Trp A:449 - Leu A:450   [ RasMol ]  
    Val A:173 - Ser A:174   [ RasMol ]  
    Val B:286 - Asn B:287   [ RasMol ]  
 

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  5ayw
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  BAMA_ECOLI | P0A940
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  BAMB_ECOLI | P77774
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  BAMC_ECOLI | P0A903
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    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  BAMD_ECOLI | P0AC02
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  BAME_ECOLI | P0A937
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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 5d0o 5d0q 5ekq 5ljo
        BAMB_ECOLI | P77774: 2yh3 2yms 3p1l 3prw 3q7m 3q7n 3q7o 4pk1 4xga 5d0o 5ljo
        BAMC_ECOLI | P0A903: 2lae 2laf 2yh5 2yh6 3sns 3tgo 5d0o 5d0q 5ekq 5ljo
        BAMD_ECOLI | P0AC02: 2yhc 3q5m 3tgo 5d0o 5d0q 5ekq 5ljo
        BAME_ECOLI | P0A937: 2km7 2kxx 2yh9 5d0o 5d0q 5ekq 5ljo

(-) Related Entries Specified in the PDB File

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