2QCZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF N-TERMINAL DOMAIN OF E. COLI YAET

Authors :   S. Kim, J. C. Malinverni, P. Sliz, T. J. Silhavy, S. C. Harrison, D. Kahne

Date :   20 Jun 07 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Potra Domain, Membrane Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kim, J. C. Malinverni, P. Sliz, T. J. Silhavy, S. C. Harrison, D. Kahne
Structure And Function Of An Essential Component Of The Outer Membrane Protein Assembly Machine.
Science V. 317 961 2007
PubMed-ID: 17702946 | Reference-DOI: 10.1126/SCIENCE.1143993
(for further references see the PDB file header)

Molecule 1 - OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR YAET
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 21-351
	Gene	:	YAET
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K-12
	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 2QCZ)

(no "Site" information available for 2QCZ)

(no "SS Bond" information available for 2QCZ)

(no "Cis Peptide Bond" information available for 2QCZ)

(no "SAP(SNP)/Variant" information available for 2QCZ)

Asymmetric Unit (1, 10)

	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	10	A:24-91 B:24-91 A:92-172 B:92-172 A:175-263 B:175-263 A:266-344 B:266-344 A:347-351 B:347-351

Biological Unit 1 (1, 5)

	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	5	A:24-91 - A:92-172 - A:175-263 - A:266-344 - A:347-351 -

Biological Unit 2 (1, 5)

	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	5	- B:24-91 - B:92-172 - B:175-263 - B:266-344 - B:347-351

(no "Exon" information available for 2QCZ)

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:310
 aligned with BAMA_ECOLI | P0A940 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:330
                                    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
           BAMA_ECOLI    22 EGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRK 351
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhh........hhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeeee.....eeeeeeee.....hhhhhhh....-----------------.hhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee......eeeeeee.....hhhhhhhhhh-.......hhhhhhhhhhhhhhhhh......eeeeeeee...--.eeeeeeee....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --POTRA  PDB: A:24-91 UniProt: 24-91                                  POTRA  PDB: A:92-172 UniProt: 92-172                                             --POTRA  PDB: A:175-263 UniProt: 175-263                                                   --POTRA  PDB: A:266-344 UniProt: 266-344                                         --POTRA PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qcz A  22 EGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQL-----------------QKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTK-EPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDA--TVKLRVNVDAGNRFYVRK 351
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       | -         -     | 221       231       241       251       261       271       281       291       301       311       321       331  |    341       351
                                                                                                                                                                                                           199               217                                                                     289 |                                     331  |                 
                                                                                                                                                                                                                                                                                                       291                                        334

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with BAMA_ECOLI | P0A940 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:330
                                    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
           BAMA_ECOLI    22 EGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRK 351
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhh.........hhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeeeee.....eeeeeeee.....hhhhhhhhhh.-----------------.hhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeee......eeeeeeeeee...hhhhhh....-...ee..hhhhhhhhhhhhhhhhh......eeeeeeee...--.eeeeeeee....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --POTRA  PDB: B:24-91 UniProt: 24-91                                  POTRA  PDB: B:92-172 UniProt: 92-172                                             --POTRA  PDB: B:175-263 UniProt: 175-263                                                   --POTRA  PDB: B:266-344 UniProt: 266-344                                         --POTRA PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qcz B  22 EGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQL-----------------QKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTK-EPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDA--TVKLRVNVDAGNRFYVRK 351
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       | -         -     | 221       231       241       251       261       271       281       291       301       311       321       331  |    341       351
                                                                                                                                                                                                           199               217                                                                     289 |                                     331  |                 
                                                                                                                                                                                                                                                                                                       291                                        334

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 2QCZ)

(no "CATH Domain" information available for 2QCZ)

(no "Pfam Domain" information available for 2QCZ)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2qcz)

	Sites
(no "Sites" information available for 2qcz)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qcz)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2qcz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BAMA_ECOLI \| P0A940
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	BAMA_ECOLI \| P0A940
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BAMA_ECOLI \| P0A940	:	2qdf 2v9h 3efc 3og5 3q6b 4c4v 4n75 4pk1 4xga 5ayw 5d0o 5d0q 5ekq 5ljo

(no "Related Entries Specified in the PDB File" available for 2QCZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 10)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File