3DSN - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE THR7PHE MUTATION IN THE GD DONOR STRAND

Authors :   L. J. Fooks, X. Yu, E. Moslehi-Mohebi, V. Tischenko, S. D. Knight, S. Macintyre, A. V. Zavialov

Date :   13 Jul 08 (Deposition) - 14 Jul 09 (Release) - 14 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Chaperone, Fimbrial Subunit, Fimbriae, Donor Strand Complementation, Protein-Protein Complex, Beta Barrel, Immunoglobulin Domain, Periplasm, Plasmid, Capsule, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. Fooks, X. Yu, E. Moslehi-Mohebi, V. Tischenko, S. D. Knight, S. Macintyre, A. V. Zavialov
Hydrophobicity And Rigidity Of Binding Segments Enable Caf1M Chaperone To Act As Assembly Catalyst
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CHAPERONE PROTEIN CAF1M
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 24 TO 258
	Gene	:	CAF1M, YPMT1.82, Y5194, Y1098, YP_PMT084
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	CAPSULE PROTEIN FRACTION 1

Molecule 2 - F1 CAPSULE ANTIGEN
	Chains	:	B, C, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 34 TO 170
	Gene	:	CAF1, YPMT1.84, Y5196, Y1100, YP_PMT082
	Mutation	:	YES
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3DSN)

(no "Site" information available for 3DSN)

Asymmetric Unit

No.	Residues
1	A:98	-	A:137
2	D:98	-	D:137

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3DSN)

Asymmetric Unit (1, 2)

	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	2	A:87-104 D:87-104

Biological Unit 1 (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 -

Biological Unit 2 (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	- D:87-104

(no "Exon" information available for 3DSN)

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:199
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:227
                                    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 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 258
               SCOP domains d3dsna1 A:9-147 Chaperone protein Caf1m                                                                                                    d3dsna2 A:148-235 Caf1m                                                                  SCOP domains
               CATH domains -----3dsnA01 A:14-145 PapD-like                                                                                                          ---3dsnA02 A:149-232  [code=2.60.40.1070, no name defined]                             --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeee.....eeeeeee.....eeeeeeeee.-------..eeee..eeee....eeeeeeee..........eeeeeeeeee...---------------------.eeeeeeeeeeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee....ee...eeeeee.........eeeeee..........eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsn A   9 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDE-------DPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPK---------------------GVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL 235
                                    18        28        38        48  |      -|       68        78        88        98      |  -         -       128       138       148       158       168       178       188       198       208       218       228       
                                                                     51      59                                           105                   127

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:149
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           CAF1_YERPE    22 ADLTASTTATATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dsnb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains 3dsnB00 B:1-149  [code=2.60.40.1 310, no name defined]                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeeee.......-........eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee..ee...........eeeeeeee.........--.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsn B   1 ADLTASFTATATLVEPARITLTYKEGAPITIM-NGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLA--KYTDAVTVTVSNQ 149
                                    10        20        30 | |    40        50        60        70        80        90       100       110       120       130   |  |140         
                                                          32 |                                                                                                 134  |            
                                                            34                                                                                                    137

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:132
                                    48        58        68        78        88        98       108       118       128       138       148       158       168  
           CAF1_YERPE    39 RITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dsnc_ C: automated matches                                                                                                         SCOP domains
               CATH domains 3dsnC00 C:18-149  [code=2.60.40.1310, no name defined]                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...ee...........eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee...............eeeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dsn C  18 RITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    27        37        47        57        67        77        87        97       107       117       127       137       147

Chain D from PDB  Type:PROTEIN  Length:190
 aligned with CAF1M_YERPE | P26926 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:225
                                    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 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNV 256
               SCOP domains d3dsnd1 D:9-147 Chaperone protein Caf1m                                                                                                    d3dsnd2 D:148-233 Caf1m                                                                SCOP domains
               CATH domains -----3dsnD01 D:14-145 PapD-like                                                                                                          ---3dsnD02 D:149-232  [code=2.60.40.1070, no name defined]                             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeee....eeeeeeee.....eeeeeeee.--------..eeee..eeee....eeeeeeee..........eeeeeeeeee...-------------------.eeeeeeeeeeeeeeeeee......hhhhhhhhheeee...eeeeee.....eeeeeeee..ee....ee...eeeeee.--------.eeeee..........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------PILI_CHAPERONE    --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsn D   9 SKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYD--------DPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPK-------------------DVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDL--------NVSWRIINDQGGLDRLYSKNV 233
                                    18        28        38        48 |       -|       68        78        88        98      |  -         -      |128       138       148       158       168       178       188       198     |   -    |  218       228     
                                                                    50       59                                           105                 125                                                                            204      213

Chain E from PDB  Type:PROTEIN  Length:149
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:149
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           CAF1_YERPE    22 ADLTASTTATATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dsne_ E: automated matches                                                                                                                          SCOP domains
               CATH domains 3dsnE00 E:1-149  [code=2.60.40.1310, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeeee................eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee...............eeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsn E   1 ADLTASFTATATLVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain F from PDB  Type:PROTEIN  Length:129
 aligned with CAF1_YERPE | P26948 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:131
                                    49        59        69        79        89        99       109       119       129       139       149       159       169 
           CAF1_YERPE    40 ITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 170
               SCOP domains d3dsnf_ F: automated matches                                                                                                        SCOP domains
               CATH domains 3dsnF00 F:19-149  [code=2.60.40.1310, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...ee...........eeeeeeee......hhh.eeee........eeeee......eeeeeeeee.....ee..ee....--.........eeeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsn F  19 ITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGEN--GDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ 149
                                    28        38        48        58        68        78        88        98       | -|      118       128       138       148 
                                                                                                                 106  |                                        
                                                                                                                    109

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1070, no name defined] (29)

Yersinia pestis. Organism_taxid: 632. (5)

1a	3dsnA02	A:149-232
1b	3dsnD02	D:149-232

Homologous Superfamily: [code=2.60.40.1310, no name defined] (6)

Yersinia pestis. Organism_taxid: 632. (4)

2a	3dsnC00	C:18-149
2b	3dsnF00	F:19-149
2c	3dsnB00	B:1-149
2d	3dsnE00	E:1-149

Homologous Superfamily: PapD-like (38)

Yersinia pestis. Organism_taxid: 632. (5)

3a	3dsnD01	D:14-145
3b	3dsnA01	A:14-145

(no "Pfam Domain" information available for 3DSN)

Asymmetric Unit(hide GO term definitions)

Chain A,D (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,C,E,F (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 Unit
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(no "Sites" information available for 3dsn)

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

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	3dsn
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1p5u	COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE ALA9ARG MUTATION IN THE GD DONOR STRAND
1z9s	NATIVE CAF1M:CAF1:CAF1 COMPLEX
3dos	COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE THR7PHE AND ALA9VAL MUTATIONS IN THE GD DONOR STRAND
3dpb	STRUCTURE OF THE COMPLEX OF THE CAF1M CHAPERONE WITH THE MINI-FIBER OF TWO CAF1 SUBUNITS (CAF1:CAF1), CARRYING THE ALA9VAL, ALA11VAL, AND LEU13VAL MUTATIONS IN THE GD DONOR STRAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 8)

CATH Domains (3, 8)

Pfam Domains (0, 0)

Gene Ontology (8, 9)

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