4B0M - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   COMPLEX OF THE CAF1AN USHER DOMAIN, CAF1M CHAPERONE AND CAF1 SUBUNIT FROM YERSINIA PESTIS

Authors :   A. Dubnovitsky, X. D. Yu, A. F. Pudney, S. Macintyre, S. D. Knight, A. V. Z

Date :   03 Jul 12 (Deposition) - 26 Sep 12 (Release) - 21 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,M

Keywords :   Protein Transport, Chaperone-Usher Pathway, Pili Assembly (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Di Yu, A. Dubnovitsky, A. F. Pudney, S. Macintyre, S. D. Knight, A. V. Zavialov
Allosteric Mechanism Controls Traffic In The Chaperone/Usher Pathway.
Structure V. 20 1861 2012
PubMed-ID: 22981947 | Reference-DOI: 10.1016/J.STR.2012.08.016

Molecule 1 - F1 CAPSULE-ANCHORING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Fragment	:	RESIDUES 23-158
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

Molecule 2 - F1 CAPSULE ANTIGEN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

Molecule 3 - CHAPERONE PROTEIN CAF1M
	Chains	:	M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Fragment	:	RESIDUES 24-258
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	CAPSULE PROTEIN FRACTION 1

		1	2	3
Asymmetric/Biological Unit	:	A	B	M

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4B0M)

(no "Site" information available for 4B0M)

Asymmetric/Biological Unit

No.	Residues
1	A:64	-	A:91
2	M:98	-	M:137

Asymmetric/Biological Unit

No.	Residues
1	Phe A:124	-	Asp A:125
2	Asp A:125	-	Gly A:126
3	Thr M:64	-	Pro M:65

(no "SAP(SNP)/Variant" information available for 4B0M)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PILI_CHAPERONE	PS00635	Gram-negative pili assembly chaperone signature.	CAF1M_YERPE	110-127	1	M:87-104

(no "Exon" information available for 4B0M)

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:131
 aligned with CAF1A_YERPE | P26949 from UniProtKB/Swiss-Prot  Length:833

    Alignment length:135
                                    32        42        52        62        72        82        92       102       112       122       132       142       152     
          CAF1A_YERPE    23 AYTFDSTMLDTNSGESIDVSLFNQGLQLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPRFDGIMPMQLWDD 157
               SCOP domains d4b0ma_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhh.....eeeeeeeee..eeeeeeeeeeeeeee..eeeeee..hhhhhhhh..hhhhhhhhh----....hhhhh...eeeee....eeeee.hhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0m A   1 AYTFDSTMLDTNSGESIDVSLFNQGLQLPGNYFVNVFVNGRKVDSGNIDFRLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLI----EQCVDLLAIPHSDVQFYFNQQKLSLIVPPQALLPRFDGIMPMQLWDD 135
                                    10        20        30        40        50        60        70        80   |    90       100       110       120       130     
                                                                                                              84   89

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:135
                                    45        55        65        75        85        95       105       115       125       135       145       155       165     
           CAF1_YERPE    36 EPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d4b0mb_ B: F1 capsule antigen Caf1                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...ee...........eeeeeeee..........eeee........eeeee......eeeeeeeee.....ee..ee...............eeeeeeeeeee.......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0m B  15 EPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    24        34        44        54        64        74        84        94       104       114       124       134       144

Chain M from PDB  Type:PROTEIN  Length:212
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:232
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
          CAF1M_YERPE    27 DIKFASKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 258
               SCOP domains d4b0mm1 M:4-147 Chaperone protein Caf1m                                                                                                         d4b0mm2 M:148-235 Caf1m                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee...eeeee.....eeeeeee.....eeeeeeee.......--..eeee..eeee....eeeeeeee..........eeeeeeeeee....----------------..eeeeeeeeeeeeeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeeee.......--.eeeee..........eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0m M   4 DIKFASKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKE--DPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKD----------------DKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAG--NVSWRIINDQGGLDRLYSKNVTL 235
                                    13        23        33        43        53  |  |  63        73        83        93       103  |      -       123       133       143       153       163       173       183       193       203      |213       223       233  
                                                                               56 59                                            106              123                                                                                    210  |                      
                                                                                                                                                                                                                                           213

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 "CATH Domain" information available for 4B0M)

(no "Pfam Domain" information available for 4B0M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAF1A_YERPE | P26949)

molecular function
	GO:0015473	fimbrial usher porin activity	A porin that acts in the assembly of fimbria together with fimbrial chaperone.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0009297	pilus assembly	The assembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies. Pili are variously involved in transfer of nucleic acids, adherence to surfaces, and formation of pellicles. Is required for bacterial conjugation, or can play a role in adherence to surfaces (when it is called a fimbrium), and in the formation of pellicles.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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.

Chain B (CAF1_YERPE | P26948)

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).
cellular component
	GO:0042603	capsule	A protective structure surrounding some fungi and bacteria, attached externally to the cell wall and composed primarily of polysaccharides. Capsules are highly organized structures that adhere strongly to cells and cannot be easily removed. Capsules play important roles in pathogenicity, preventing phagocytosis by other cells, adherance, and resistance to dessication.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain M (CAF1M_YERPE | P26926)

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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0061077	chaperone-mediated protein folding	The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
	GO:0043711	pilus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological 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 4b0m)

	Sites
(no "Sites" information available for 4b0m)

	Cis Peptide Bonds
		Asp A:125 - Gly A:126	[ RasMol ]
		Phe A:124 - Asp A:125	[ RasMol ]
		Thr M:64 - Pro M:65	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	4b0m
		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
	CAF1A_YERPE \| P26949
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CAF1M_YERPE \| P26926
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CAF1_YERPE \| P26948
		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
	CAF1A_YERPE \| P26949
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CAF1M_YERPE \| P26926
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CAF1_YERPE \| P26948
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CAF1A_YERPE \| P26949	:	2xet 3fcg 4b0e
	CAF1M_YERPE \| P26926	:	1p5u 1p5v 1z9s 2os7 3dos 3dpb 3dsn 4ay0 4ayf 4az8
	CAF1_YERPE \| P26948	:	1p5u 1p5v 1z9s 3dos 3dpb 3dsn 4ayf 4az8

1p5u	X-RAY STRUCTURE OF THE TERNARY CAF1M:CAF1: CAF1CHAPERONE:SUBUNIT:SUBUNIT COMPLEX
1p5v	X-RAY STRUCTURE OF THE CAF1M:CAF1 CHAPERONE: SUBUNITPREASSEMBLY COMPLEX
1z9s	CRYSTAL STRUCTURE OF THE NATIVE CHAPERONE:SUBUNIT: SUBUNITCAF1M:CAF1:CAF1 COMPLEX
2xet	CONSERVED HYDROPHOBIC CLUSTERS ON THE SURFACE OF THE CAF1A USHER C-TERMINAL DOMAIN ARE IMPORTANT FOR F1 ANTIGEN ASSEMBLY
4ay0	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MONOMERIC SUBUNIT-FREE CAF1M CHAPERONE
4ayf	CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M:CAF1 CHAPERONE:SUBUNIT PREASSEMBLY COMPLEX CARRYING THE TYR40ALA MUTATION IN THE CAF1M CHAPERONE
4az8	CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M:CAF1 CHAPERONE:SUBUNIT PREASSEMBLY COMPLEX CARRYING THE KDKDTN INSERTION AT THE F1G1 LOOP REGION
4b0e	CRYSTAL STRUCTURE OF THE CAF1A USHER PROTEIN N- TERMINAL DOMAIN FROM YERSINIA PESTIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 17)

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