3TGO - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE E. COLI BAMCD COMPLEX

Authors :   M. Paetzel, K. H. Kim, S. Aulakh

Date :   17 Aug 11 (Deposition) - 28 Sep 11 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)
Biol. Unit 4: A,B,C,D  (2x)

Keywords :   Lipoprotein Complex, Tpr Repeat, Helix-Grip Fold, Outer Membrane Protein Assembly, Outer Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Kim, S. Aulakh, M. Paetzel
Crystal Structure Of The Beta-Barrel Assembly Machinery Bamcd Protein Complex
J. Biol. Chem. V. 286 39116 2011
PubMed-ID: 21937441 | Reference-DOI: 10.1074/JBC.M111.298166

Molecule 1 - UPF0169 LIPOPROTEIN YFIO
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-245
	Gene	:	B2595, JW2577, YFIO
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Molecule 2 - LIPOPROTEIN 34
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-344
	Gene	:	B2477, DAPX, JW2462, NLPB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D
Biological Unit 3 (1x)	:	A	B	C	D
Biological Unit 4 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	K	1	Ligand/Ion	POTASSIUM ION
4	NA	1	Ligand/Ion	SODIUM ION
5	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (2, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:121 , ASP C:38	BINDING SITE FOR RESIDUE K A 1
2	AC2	SOFTWARE	GLY A:65 , PRO A:66 , SER A:68 , HOH A:274	BINDING SITE FOR RESIDUE GOL A 4
3	AC3	SOFTWARE	TYR A:185 , ARG A:197 , ARG B:94 , ARG B:97	BINDING SITE FOR RESIDUE CL B 1
4	AC4	SOFTWARE	LYS B:233 , HOH B:270	BINDING SITE FOR RESIDUE GOL B 3
5	AC5	SOFTWARE	LYS C:127 , HOH C:358 , HOH C:361 , LYS D:127	BINDING SITE FOR RESIDUE PO4 C 1
6	AC6	SOFTWARE	ASN C:128 , THR C:130 , ASN D:128 , THR D:130	BINDING SITE FOR RESIDUE NA D 1
7	AC7	SOFTWARE	LYS A:233 , GLN B:69 , ARG D:96	BINDING SITE FOR RESIDUE GOL D 345
8	AC8	SOFTWARE	MET B:117 , ASP B:121 , GLY D:37 , ASP D:38 , TYR D:41	BINDING SITE FOR RESIDUE GOL D 2

(no "SS Bond" information available for 3TGO)

Asymmetric Unit

No.	Residues
1	Gly C:72	-	Ser C:73
2	Gly C:169	-	Tyr C:170
3	Tyr C:170	-	Gln C:171
4	Thr D:70	-	Asn D:71
5	Tyr D:170	-	Gln D:171

(no "SAP(SNP)/Variant" information available for 3TGO)

(no "PROSITE Motif" information available for 3TGO)

(no "Exon" information available for 3TGO)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:217
 aligned with BAMD_ECOLI | P0AC02 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:217
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       
           BAMD_ECOLI    26 EVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS 242
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tgo A  26 EVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS 242
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with BAMD_ECOLI | P0AC02 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:218
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235        
           BAMD_ECOLI    26 EVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS 243
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tgo B  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 C from PDB  Type:PROTEIN  Length:182
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:186
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
           BAMC_ECOLI    28 DSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSA 213
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh....hhhhhh...............................hhhhh...............eeeee..eeeeee.----..hhhhhhhhhhhh...eeeee....eeeeeeee.........eeeeeeeeeee....eeeeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tgo C  28 DSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVE----NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSA 213
                                    37        47        57        67        77        87        97       107 |    |117       127       137       147       157       167       177       187       197       207      
                                                                                                           109  114

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with BAMC_ECOLI | P0A903 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:190
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
           BAMC_ECOLI    28 DSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAA 217
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh...............................hhhhh...............eeeee..eeeeee.----..hhhhhhhhhhhhh..eeeee....eeee..ee.........eeeeeeeeeee....eeeeeeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tgo D  28 DSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVE----NTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAA 217
                                    37        47        57        67        77        87        97       107 |    |117       127       137       147       157       167       177       187       197       207       217
                                                                                                           109  114

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 '\|'

(no "SCOP Domain" information available for 3TGO)

(no "CATH Domain" information available for 3TGO)

(no "Pfam Domain" information available for 3TGO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BAMD_ECOLI | P0AC02)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0043165	Gram-negative-bacterium-type cell outer membrane assembly	The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0051205	protein insertion into membrane	The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
cellular component
	GO:1990063	Bam protein complex	Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex.
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain C,D (BAMC_ECOLI | P0A903)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0043165	Gram-negative-bacterium-type cell outer membrane assembly	The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0051205	protein insertion into membrane	The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
cellular component
	GO:1990063	Bam protein complex	Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex.
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly C:169 - Tyr C:170	[ RasMol ]
		Gly C:72 - Ser C:73	[ RasMol ]
		Thr D:70 - Asn D:71	[ RasMol ]
		Tyr C:170 - Gln C:171	[ RasMol ]
		Tyr D:170 - Gln D:171	[ RasMol ]

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2laf	N-TERMINAL DOMAIN STRUCTURE OF E. COLI BAMC (NMR)
2yh6	N-TERMINAL DOMAIN STRUCTURE OF E. COLI BAMC (X-RAY)
2yhc	CRYSTAL STRUCTURE OF E. COLI BAMD
3qky	CRYSTAL STRUCTURE OF R. MARINUS BAMD
3sns	C-TERMINAL DOMAIN OF THE E. COLI BAMC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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