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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE COLICIN I RECEPTOR CIR FROM E.COLI

Authors :   S. K. Buchanan, L. Esser, P. Lukacik

Date :   20 Jun 06 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A

Keywords :   Outer Membrane, Iron Transport, Tonb Box, Signal Transduction, Colicin I Receptor, Membrane Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Buchanan, P. Lukacik, S. Grizot, R. Ghirlando, M. M. Ali, T. J. Barnard, K. S. Jakes, P. K. Kienker, L. Esser
Structure Of Colicin I Receptor Bound To The R-Domain Of Colicin Ia: Implications For Protein Import.
Embo J. V. 26 2594 2007
PubMed-ID: 17464289 | Reference-DOI: 10.1038/SJ.EMBOJ.7601693

Molecule 1 - COLICIN I RECEPTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET20B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	COLICIN I RECEPTOR
	Gene	:	CIRA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	OES	2	Ligand/Ion	N-OCTYL-2-HYDROXYETHYL SULFOXIDE
3	SR	1	Ligand/Ion	STRONTIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:123 , TRP A:124 , SER A:234 , ASP A:236 , ASP A:258	BINDING SITE FOR RESIDUE SR A 23
2	AC2	SOFTWARE	TYR A:362 , MSE A:384 , GLU A:392 , ASN A:495 , ARG A:513	BINDING SITE FOR RESIDUE OES A 21
3	AC3	SOFTWARE	TYR A:277 , TYR A:294 , GLU A:313 , ASN A:315	BINDING SITE FOR RESIDUE OES A 22

Asymmetric/Biological Unit

No.	Residues
1	A:435	-	A:439

Asymmetric/Biological Unit

No.	Residues
1	Pro A:63	-	Val A:64
2	Glu A:82	-	Gly A:83
3	Asp A:84	-	Asn A:85
4	Lys A:212	-	Asp A:213
5	Ile A:229	-	Glu A:230
6	Glu A:230	-	Gly A:231
7	Asp A:345	-	Ala A:346
8	Gln A:501	-	Asn A:502
9	Ala A:510	-	Asn A:511
10	Leu A:568	-	Pro A:569
11	Ala A:583	-	Leu A:584

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TONB_DEPENDENT_REC_2	PS01156	TonB-dependent receptor proteins signature 2.	CIRA_ECOLI	646-663	1	A:647-663

(no "Exon" information available for 2HDF)

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:584
 aligned with CIRA_ECOLI | P17315 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:634
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    
           CIRA_ECOLI    30 GETMVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAVFRHNDFDLNWIPVDSIERIEVVRGPMSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGMKAYGSLAKREKDDPQNSTTTDTGETPRIEGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDSDSLDKNRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNPGNSSPITSESNTVDGKYTLPLTAINQFLTVGGEWRHDKLSDAVNLTGGTSSKTSASQYALFVEDEWRIFEPLALTTGVRMDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYMGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSFYVSGHYTGQKRADSATAKTPGGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSRDDYSYNEDGRRYFMAVDYRF 663
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hdfA01 A:30-157 Ferric Hydroxamate Uptake Protein; Chain A, domain 1                                                           -----2hdfA02 A:163-663  [code=2.40.170.20, no name defin              ed]                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee.hhh..eeeeehhhhhh.....hhhhhhh....eeee.......eeee...hhhhheeee..ee.......--------...hhh.eeeeeeee..hhhhhhhhhh..eeeeee.......eeeeeeeeeee.......eeeeeeeeeeeee...eeeeeeeeeeee...--------------....eeeeeeeeeeeeeee..eeeeeeeeeeeeee...--...eeeeeeeeeeeeeee..eeeeeeeeeeeeeee..---..eeeeeeeeeeeeeeeehhh.eeeeeeeeeeeeee....-------.....eeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeee..hhhhhh...eeeehhhheeee.......eeeeeeeeeeeee.........eeeeeeeeeeeeeeee........hhhhh..eeeee.......eeeee.eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeee.hhhh.ee.....eeeeeeeeee.......eeeeeeeeee.------------...eeeeeeeee.....eeeeeeee........----.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hdf A  30 GETmVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAV--------NWIPVDSIERIEVVRGPmSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGmKAYGSLAKREKD--------------RIEGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDSD--DKNRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNP---SPITSESNTVDGKYTLPLTAINQFLTVGGEmRHDKmSDAV-------SKTSASQYALFVEDEWRIFEPLALTTGVRmDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYmGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSmYmSGHYTG------------GGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLS----SYNEDGRRYFmAVDYRF 663
                               |    39        49        59        69        79        89        99       109    |    -   |   129       139|      149       159       169       179       189       199 |     209   |     -       229       239       249       259     | 269       279       289       299    |  309       319       329       339   |   | -     | 359       369       379    |  389       399       409       419       429       439       449       459  |    469       479       489       499       509       519       529       539       549       559       569       579       589 |     | -         -|      619       629       639  |    649       659    
                               |                                                                              114      123              140-MSE                                                      201-MSE     213            228                                  265  |                                 304 308                           338-MSE| 347     355                          384-MSE                                                                       462-MSE                                                                                                                        589-MSE 597          610                             642  647       657-MSE  
                              33-MSE                                                                                                                                                                                                                                    268                                                                        343-MSE                                                                                                                                                                                                                                                 591-MSE

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 2HDF)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CIRA_ECOLI | P17315)

molecular function
	GO:0042912	colicin transmembrane transporter activity	Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0015343	siderophore transmembrane transporter activity	Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).
biological process
	GO:0043213	bacteriocin transport	The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0033212	iron assimilation	A process in which iron is solubilized and transported into a cell.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0044718	siderophore transmembrane transport	The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:510 - Asn A:511	[ RasMol ]
		Ala A:583 - Leu A:584	[ RasMol ]
		Asp A:345 - Ala A:346	[ RasMol ]
		Asp A:84 - Asn A:85	[ RasMol ]
		Gln A:501 - Asn A:502	[ RasMol ]
		Glu A:230 - Gly A:231	[ RasMol ]
		Glu A:82 - Gly A:83	[ RasMol ]
		Ile A:229 - Glu A:230	[ RasMol ]
		Leu A:568 - Pro A:569	[ RasMol ]
		Lys A:212 - Asp A:213	[ RasMol ]
		Pro A:63 - Val A:64	[ RasMol ]

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Access by PDB/NDB ID
	2hdf
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UniProtKB/Swiss-Prot
	CIRA_ECOLI \| P17315	:	2hdi

2hdi	THE SAME PROTEIN IN COMPLEX WITH THE R-DOMAIN OF COLICIN IA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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Gene Ontology (12, 12)

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