4C4V - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE OUTER MEMBRANE PROTEIN INSERTASE BAMA WITH ONE POTRA DOMAIN.

Authors :   K. Zeth, R. Albrecht, K. Diederichs

Date :   09 Sep 13 (Deposition) - 23 Apr 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Protein Transport, Omp85 Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Albrecht, M. Schuetz, P. Oberhettinger, M. Faulstich, I. Bermejo, T. Rudel, K. Diederichs, K. Zeth
Structure Of Bama, An Essential Factor In Outer Membrane Protein Biogenesis
Acta Crystallogr. , Sect. D V. 70 1779 2014
PubMed-ID: 24914988 | Reference-DOI: 10.1107/S1399004714007482

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET30B
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAMA TRUNCATED BY 4 POTRA DOMAINS, RESIDUES 347-808
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	OUTER MEMBRANE PROTEIN BAMA FROM E. COLI TRUNCATED BY POTRA DOMAIN 1
	Synonym	:	OMP85

Molecule 2 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET30B
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAMA TRUNCATED BY 4 POTRA DOMAINS, RESIDUES 344-808
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	OUTER MEMBRANE PROTEIN BAMA FROM E. COLI TRUNCATED BY POTRA DOMAIN 1
	Synonym	:	OMP85

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4C4V)

(no "Site" information available for 4C4V)

(no "SS Bond" information available for 4C4V)

Asymmetric Unit

No.	Residues
1	Trp A:449	-	Leu A:450
2	Thr A:452	-	Gly A:453
3	Tyr A:477	-	Phe A:478
4	Thr B:479	-	Val B:480
5	Asp B:481	-	Gly B:482
6	Lys B:644	-	Glu B:645
7	Ser B:726	-	Asp B:727
8	Gly B:807	-	Lys B:808

(no "SAP(SNP)/Variant" information available for 4C4V)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTRA	PS51779	POTRA domain profile.	BAMA_ECOLI	24-91 92-172 175-263 266-344 347-421	2	- - - - A:347-421 B:347-421

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTRA	PS51779	POTRA domain profile.	BAMA_ECOLI	24-91 92-172 175-263 266-344 347-421	1	- - - - A:347-421 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POTRA	PS51779	POTRA domain profile.	BAMA_ECOLI	24-91 92-172 175-263 266-344 347-421	1	- - - - - B:347-421

(no "Exon" information available for 4C4V)

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:445
 aligned with BAMA_ECOLI | P0A940 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:462
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806  
           BAMA_ECOLI   347 FYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK 808
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhh.........hhhhhhhhhhhhhhh..eeeeeeeeee......eeeeeeeeee....eee..eeee.....ee..eeee........eeeeeeee...eeeeeeeee..........eeeeeeeeeee.........eeeeeeeeeeeee.....eeeeeeeeeeeeeee....hhhhhhhhhhh...........eeeeeeeeeeeeeeee..........eeeeeeeeeee........eeeeeeeeeeee.......eeeeeeeeeeee.......hhhhh..........ee.......eeee......---------------....eeeeee....eeeeeeeeeee......hhhhh.eeeeeeeeeeeee.......--............eeeeeeeeeeee..eeeeeeeeeeee......ee.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE POTRA  PDB: A:347-421 UniProt: 347-421                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c4v A 347 FYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADSSDYTNKSYGTDVTLGFPINEENSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAIYFPHQAS---------------AKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSS--SGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK 808
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676   |     -       696       706       716       726       736       746     | 756       766       776       786       796       806  
                                                                                                                                                                                                                                                                                                                                                                       680             696                                                     752  |                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                  755

Chain B from PDB  Type:PROTEIN  Length:446
 aligned with BAMA_ECOLI | P0A940 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:465
                                   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     
           BAMA_ECOLI   344 GNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK 808
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhh.........hhhhhhhhhhhhhhh..eeeeeeeeee......eeeeeeeeee....eee..eeee.....ee..eeee........eeeeeeee...eeeeeeeeee.........eeeeeeeeeee.........eeeeeeeeeeeee.....eeeeeeeeeeeeeee....hhhhhhhhh.............eeeeeeeeeeeeeeee..........eeeeeeeeeee........eeeeeeeeeeee.......eeeeeeeeeeee.......hhhhh..........ee...............-------------------............eeeeeeeeeee......hhhhh.eeeeeeeeeeeee.....................eeeeeeeeeeee..eeeeeeeeeeee......ee.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE P--POTRA  PDB: B:347-421 UniProt: 347-421                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c4v B 344 GNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADSSDYTNKSYGTDVTLGFPINEENSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAIYFPHQ-------------------DLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK 808
                                   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    |    -         -    |  703       713       723       733       743       753       763       773       783       793       803     
                                                                                                                                                                                                                                                                                                                                                                        678                 698

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 4C4V)

(no "CATH Domain" information available for 4C4V)

(no "Pfam Domain" information available for 4C4V)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BAMA_ECOLI | P0A940)

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:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0071709	membrane assembly	The aggregation, arrangement and bonding together of a set of components to form a membrane.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4c4v)

	Sites
(no "Sites" information available for 4c4v)

	Cis Peptide Bonds
		Asp B:481 - Gly B:482	[ RasMol ]
		Gly B:807 - Lys B:808	[ RasMol ]
		Lys B:644 - Glu B:645	[ RasMol ]
		Ser B:726 - Asp B:727	[ RasMol ]
		Thr A:452 - Gly A:453	[ RasMol ]
		Thr B:479 - Val B:480	[ RasMol ]
		Trp A:449 - Leu A:450	[ RasMol ]
		Tyr A:477 - Phe A:478	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4c4v
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	BAMA_ECOLI \| P0A940	:	2qcz 2qdf 2v9h 3efc 3og5 3q6b 4n75 4pk1 4xga 5ayw 5d0o 5d0q 5ekq 5ljo

(no "Related Entries Specified in the PDB File" available for 4C4V)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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Exons (0, 0)

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