4AZ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M:CAF1 CHAPERONE:SUBUNIT PREASSEMBLY COMPLEX CARRYING THE KDKDTN INSERTION AT THE F1G1 LOOP REGION

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

Date :   24 Jun 12 (Deposition) - 26 Sep 12 (Release) - 21 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Chaperone-Immune System Complex, Antigens, Fimbriae, Molecular Chaperones (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 - CHAPERONE PROTEIN CAF1M
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFM1-M-INSA114-KDKDTN
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PTRC99A
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 24-258
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	CAPSULE PROTEIN FRACTION 1

Molecule 2 - F1 CAPSULE ANTIGEN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFM1-M-INSA114-KDKDTN
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PTRC99A
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4AZ8)

(no "Site" information available for 4AZ8)

Asymmetric/Biological Unit

No.	Residues
1	A:98	-	A:137

Asymmetric/Biological Unit

No.	Residues
1	Thr A:64	-	Pro A:65

(no "SAP(SNP)/Variant" information available for 4AZ8)

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	A:87-104

(no "Exon" information available for 4AZ8)

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:186
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:226
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
          CAF1M_YERPE    32 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVT 257
               SCOP domains d4az8a1 A:9-147 automated matches                                                                                                          d4az8a2 A:148-23  4 automated matches                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeee.....eeeeeee.....eeeeeeee.----------.eee..eeee....eeeeeee.----......eeeeeeeeee..---------------------.eeeeeeeeeeeeeeeee......hhhhhhhhheeee.--.eeeee.......eeeeee..ee.........eeeee...---....eeeeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------PILI_CHAPERONE    ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4az8 A   9 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYD----------FVVTPPLFRLDAKQQNSLRIAQ----FPRDKESLKWLCVKGIPP---------------------VGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVD--KLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLP---AGARNVSWRIINDQGGLDRLYSKNVT 234
                                    18        28        38        48 |       -  |     68        78   |    88        98     |   -         -       128       138       148       158    |  168       178       188       198      |  -|      218       228      
                                                                    50         61                   82   87              104                   126                                  163  |                                    205 209                         
                                                                                                                                                                                       166

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:134
                                    45        55        65        75        85        95       105       115       125       135       145       155       165    
           CAF1_YERPE    36 EPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSN 169
               SCOP domains d4az8b_ B: F1 cap    sule antigen Caf1                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......----......eeeeeeee...---hhh.eeee........eeeee......eeeeeeeee..-..ee..ee...............eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4az8 B  15 EPARITLTYKEGAPITI----NIDTELLVGTLTLGGYK---TSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDS-DFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSN 148
                                    24      |  - |      44       | - |      64        74        84        |-|      104       114       124       134       144    
                                           31   36              52  56                                   93 |                                                     
                                                                                                           95

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 4AZ8)

(no "Pfam Domain" information available for 4AZ8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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).

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4az8)

	Sites
(no "Sites" information available for 4az8)

	Cis Peptide Bonds
		Thr A:64 - Pro A:65	[ RasMol ]

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	4az8
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	CAF1M_YERPE \| P26926
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	CAF1_YERPE \| P26948
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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
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
4b0e	CRYSTAL STRUCTURE OF THE CAF1A USHER PROTEIN N- TERMINAL DOMAIN FROM YERSINIA PESTIS
4b0m	COMPLEX OF THE CAF1AN USHER DOMAIN, CAF1M CHAPERONE AND CAF1 SUBUNIT FROM YERSINIA PESTIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 9)

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