4DWH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE MAJOR TYPE 1 PILUS SUBUNIT FIMA BOUND TO THE FIMC (2.5 A RESOLUTION)

Authors :   M. A. Scharer, C. Puorger, M. Crespo, R. Glockshuber, G. Capitani

Date :   24 Feb 12 (Deposition) - 30 May 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Protein-Chaperone Complex, Immunoglobin-Like Fold, Involved In Type 1 Pilus Assembly, Structural Protein-Chaperone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Crespo, C. Puorger, M. A. Scharer, O. Eidam, M. G. Grutter, G. Capitani, R. Glockshuber
Quality Control Of Disulfide Bond Formation In Pilus Subunits By The Chaperone Fimc.
Nat. Chem. Biol. V. 8 707 2012
PubMed-ID: 22772153 | Reference-DOI: 10.1038/NCHEMBIO.1019

Molecule 1 - CHAPERONE PROTEIN FIMC
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFIMC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B4316, FIMC, JW4279
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - TYPE-1 FIMBRIAL PROTEIN, A CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFIMAT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B4314, FIMA, JW4277, PILA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TYPE-1A PILIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	PEG	10	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	PEG	7	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:124 , LEU A:150 , ASN A:191 , ASP A:192 , HOH A:422 , HOH A:428	BINDING SITE FOR RESIDUE PEG A 301
02	AC2	SOFTWARE	LEU A:32 , ILE A:90 , SER A:92	BINDING SITE FOR RESIDUE PEG A 302
03	AC3	SOFTWARE	TRP A:36 , LYS A:44	BINDING SITE FOR RESIDUE PEG A 303
04	AC4	SOFTWARE	ARG A:79 , GLN B:44 , GLU B:45 , ALA B:47 , ARG B:106	BINDING SITE FOR RESIDUE PEG A 304
05	AC5	SOFTWARE	LYS A:119 , MET A:200 , THR A:201	BINDING SITE FOR RESIDUE PEG A 305
06	AC6	SOFTWARE	ASN A:73 , GLN A:77 , PG4 A:307 , GLN B:57	BINDING SITE FOR RESIDUE PEG A 306
07	AC7	SOFTWARE	ASN A:25 , ASP A:26 , PEG A:306 , ASN B:59	BINDING SITE FOR RESIDUE PG4 A 307
08	AC8	SOFTWARE	MET A:57 , LYS A:58 , LYS A:61 , LYS C:58	BINDING SITE FOR RESIDUE PO4 A 308
09	AC9	SOFTWARE	ILE A:190 , GLY A:194 , LEU A:196 , ASN B:18 , ASP B:62 , ASN B:64 , HOH B:314	BINDING SITE FOR RESIDUE PEG B 201
10	BC1	SOFTWARE	GLY A:5 , ALA A:6 , TYR A:193 , MET B:17 , ASN B:18	BINDING SITE FOR RESIDUE PO4 B 202
11	BC2	SOFTWARE	ASN C:28 , SER C:92 , MET C:93 , ASP D:29	BINDING SITE FOR RESIDUE PEG C 301
12	BC3	SOFTWARE	ASN A:24 , ASN C:24 , LYS C:60	BINDING SITE FOR RESIDUE PGE C 302
13	BC4	SOFTWARE	PRO C:124 , LEU C:150 , ILE C:190 , ASN C:191 , ASP C:192 , HOH C:425	BINDING SITE FOR RESIDUE PGE C 303
14	BC5	SOFTWARE	ALA C:21 , GLU C:62	BINDING SITE FOR RESIDUE PEG C 304
15	BC6	SOFTWARE	ASN C:25 , ASP C:26 , ASP D:24 , GLY D:26 , SER D:27 , ASN D:59 , ASP D:60	BINDING SITE FOR RESIDUE PG4 D 201
16	BC7	SOFTWARE	PRO C:91 , GLN C:104 , ASP D:151 , ALA D:152	BINDING SITE FOR RESIDUE PEG D 202

Asymmetric Unit

No.	Residues
1	B:21	-	B:61
2	D:21	-	D:61

Asymmetric Unit

No.	Residues
1	Thr A:51	-	Pro A:52
2	Phe B:118	-	Ser B:119
3	Thr C:51	-	Pro C:52

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_FIMC_ECOLI_002 *	E	54	V	FIMC_ECOLI	---	---	A/C	E	18	V
2	UniProt	VAR_FIMC_ECOLI_003 *	T	210	A	FIMC_ECOLI	---	---	A/C	T	174	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_FIMC_ECOLI_002 *	E	54	V	FIMC_ECOLI	---	---	A	E	18	V
2	UniProt	VAR_FIMC_ECOLI_003 *	T	210	A	FIMC_ECOLI	---	---	A	T	174	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_FIMC_ECOLI_002 *	E	54	V	FIMC_ECOLI	---	---	C	E	18	V
2	UniProt	VAR_FIMC_ECOLI_003 *	T	210	A	FIMC_ECOLI	---	---	C	T	174	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	FIMC_ECOLI	111-128	2	A:75-92 C:75-92

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.	FIMC_ECOLI	111-128	1	A:75-92 -

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.	FIMC_ECOLI	111-128	1	- C:75-92

(no "Exon" information available for 4DWH)

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:197
 aligned with FIMC_ECOLI | P31697 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:204
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
           FIMC_ECOLI    37 GVALGATRVIYPAGQKQEQLAVTNNDENSTYLIQSWVENADGVKDGRFIVTPPLFAMKGKKENTLRILDATNNQLPQDRESLFWMNVKAIPSMDKSKLTENTLQLAIISRIKLYYRPAKLALPPDQAAEKLRFRRSANSLTLINPTPYYLTVTELNAGTRVLENALVPPMGESTVKLPSDAGSNITYRTINDYGALTPKMTGVM 240
               SCOP domains d4dwha1 A:1-121 Periplasmic chaperone FimC                                                                               d4dwha2 A:122-204 FimC                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee.....eeeeeeeeee........eeee..eeeee..eeeeeeeee...........eeeeeeeeeee...-----..eeeeeeeeeeeeeee......hhhhhhhhheeee...eeeee......eeeeeeee..ee...eee....eeeee...--..eeeeee..........eeee. Sec.struct. author
                 SAPs(SNPs) -----------------V-----------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------PILI_CHAPERONE    ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dwh A   1 GVALGATRVIYPAGQKQEQLAVTNNDENSTYLIQSWVENADGVKDGRFIVTPPLFAMKGKKENTLRILDATNNQLPQDRESLFWMNVKAIPSMD-----ENTLQLAIISRIKLYYRPAKLALPPDQAAEKLRFRRSANSLTLINPTPYYLTVTELNAGTRVLENALVPPMGESTVKLPS--GSNITYRTINDYGALTPKMTGVM 204
                                    10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170        |- |     190       200    
                                                                                                                        94   100                                                                            179  |                      
                                                                                                                                                                                                               182

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with FIMA1_ECOLI | P04128 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:143
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179   
          FIMA1_ECOLI    40 VNAACAVDAGSVDQTVQLGQVRTASLAQEGATSSAVGFNIQLNDCDTNVASKAAVAFLGTAIDAGHTNVLALQSSAAGSATNVGVQILDRTGAALTLDGATFSSETTLNNGTNTIPFQARYFATGAATPGAANADATFKVQYQ 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eee...........eeee...eeeeeeee..hhhhhhh.eeeee................----..eeeeeeee................------...eeeeeeeeeeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwh B  17 MNAACAVDAGSVDQTVQLGQVRTASLAQEGATSSAVGFNIQLNDCDTNVASKAAVAFLGTAIDAGHTNVLALQS----SATNVGVQILDRTGAALTLDGATFSS------GTNTIPFQARYFATGAATPGAANADATFKVQYQ 159
                                    26        36        46        56        66        76        86   |    96       106       116   |     -|      136       146       156   
                                                                                                    90   95                      120    127

Chain C from PDB  Type:PROTEIN  Length:201
 aligned with FIMC_ECOLI | P31697 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:205
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236     
           FIMC_ECOLI    37 GVALGATRVIYPAGQKQEQLAVTNNDENSTYLIQSWVENADGVKDGRFIVTPPLFAMKGKKENTLRILDATNNQLPQDRESLFWMNVKAIPSMDKSKLTENTLQLAIISRIKLYYRPAKLALPPDQAAEKLRFRRSANSLTLINPTPYYLTVTELNAGTRVLENALVPPMGESTVKLPSDAGSNITYRTINDYGALTPKMTGVME 241
               SCOP domains d4dwhc1 C:1-121 Periplasmic chaperone FimC                                                                               d4dwhc2 C:122-205 FimC                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee.....eeeeeee.....eeeeeeeee.........eeee..eeeee...eeeeeeee...........eeeeeeeeeee....----..eeeeeeeeeeeeeee......hhhhhhhhheeeee..eeeeee.....eeeeeeee..ee...eee...eeeeee.......eeeeee..........eeeeee Sec.struct. author
                 SAPs(SNPs) -----------------V-----------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------PILI_CHAPERONE    ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwh C   1 GVALGATRVIYPAGQKQEQLAVTNNDENSTYLIQSWVENADGVKDGRFIVTPPLFAMKGKKENTLRILDATNNQLPQDRESLFWMNVKAIPSMDK----ENTLQLAIISRIKLYYRPAKLALPPDQAAEKLRFRRSANSLTLINPTPYYLTVTELNAGTRVLENALVPPMGESTVKLPSDAGSNITYRTINDYGALTPKMTGVME 205
                                    10        20        30        40        50        60        70        80        90    |  100       110       120       130       140       150       160       170       180       190       200     
                                                                                                                         95  100

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with FIMA1_ECOLI | P04128 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:143
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179   
          FIMA1_ECOLI    40 VNAACAVDAGSVDQTVQLGQVRTASLAQEGATSSAVGFNIQLNDCDTNVASKAAVAFLGTAIDAGHTNVLALQSSAAGSATNVGVQILDRTGAALTLDGATFSSETTLNNGTNTIPFQARYFATGAATPGAANADATFKVQYQ 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eee..................eeeeeeee..hhhhhhheeeeee................---.....eeeeee.............ee..------..eeeeeeeeee..........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwh D  17 MNAACAVDAGSVDQTVQLGQVRTASLAQEGATSSAVGFNIQLNDCDTNVASKAAVAFLGTAIDAGHTNVLALQS---GSATNVGVQILDRTGAALTLDGATFSSE------TNTIPFQARYFATGAATPGAANADATFKVQYQ 159
                                    26        36        46        56        66        76        86   |   |96       106       116    |    - |     136       146       156   
                                                                                                    90  94                        121    128

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: Periplasmic chaperone C-domain (38)

Family: Periplasmic chaperone C-domain (33)

Protein domain: FimC (8)

Escherichia coli [TaxId: 562] (8)

1a	d4dwha2	A:122-204
1b	d4dwhc2	C:122-205

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: PapD-like (47)

Family: Pilus chaperone (36)

Protein domain: Periplasmic chaperone FimC (8)

Escherichia coli [TaxId: 562] (8)

2a	d4dwha1	A:1-121
2b	d4dwhc1	C:1-121

(no "CATH Domain" information available for 4DWH)

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (FIMC_ECOLI | P31697)

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).
	GO:0044183	protein binding involved in protein folding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
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,D (FIMA1_ECOLI | P04128)

biological process
	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.
cellular component
	GO:0009289	pilus	A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe B:118 - Ser B:119	[ RasMol ]
		Thr A:51 - Pro A:52	[ RasMol ]
		Thr C:51 - Pro C:52	[ RasMol ]

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	4dwh
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UniProtKB/Swiss-Prot
	FIMA1_ECOLI \| P04128	:	2jty 2m5g 2n7h 3sqb
	FIMC_ECOLI \| P31697	:	1bf8 1kiu 1klf 1qun 1ze3 3bwu 3jwn 3rfz 3sqb 4j3o

3sqb	THE SAME STRUCTURE IN A DIFFERENT SPACE GROUP AT 3.2 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (2, 4)

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Gene Ontology (9, 9)

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