3RFZ | pdb_00003rfz

Crystal structure of the FimD usher bound to its cognate FimC:FimH substrate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d3rfzf1	All beta proteins	Immunoglobulin-like beta-sandwich	PapD-like	Pilus chaperone	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d3rfzf2	All beta proteins	C2 domain-like	Periplasmic chaperone C-domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3rfzc1	All beta proteins	Immunoglobulin-like beta-sandwich	PapD-like	Pilus chaperone	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3rfzc2	All beta proteins	C2 domain-like	Periplasmic chaperone C-domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d3rfzd1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Bacterial adhesins	Pilus subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3rfza1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Bacterial adhesins	Pilus subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Periplasmic chaperone C-domain	8035665	3000998	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PapD-like	8055315	3002067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Periplasmic chaperone C-domain	8035665	3000998	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PapD-like	8055315	3002067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FimD/Slr0280 N-terminal domain-like	8039575	3001001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FimD/Slr0280 N-terminal domain-like	8039575	3001001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial adhesin-like	8032980	3000723	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial adhesin-like	8032980	3000723	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Flavin_Reduct	e3rfzF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
C	Anemone_cytotox	e3rfzC1	A: alpha bundles	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Anemone_cytotox	ECOD (develop294)
E	Ribonuclease_3	e3rfzE2	A: alpha bundles	X: RNase III catalytic domain-like	H: RNase III catalytic domain-like	T: RNase III catalytic domain-like	F: Ribonuclease_3	ECOD (develop294)
E	UvrA_DNA-bind	e3rfzE1	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: UvrA_DNA-bind	ECOD (develop294)
B	RA	e3rfzB1	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA	ECOD (develop294)
B	UvrA_DNA-bind	e3rfzB2	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: UvrA_DNA-bind	ECOD (develop294)
D	Flavin_Reduct	e3rfzD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
A	Flavin_Reduct	e3rfzA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	3.10.20.410	Alpha Beta	Roll	Ubiquitin-like (UB roll)	PapC, N-terminal domain	CATH (4.3.0)
E	2.60.40.3110	Mainly Beta	Sandwich	Immunoglobulin-like	Outer membrane usher protein	CATH (4.3.0)
E	2.60.40.2610	Mainly Beta	Sandwich	Immunoglobulin-like	Outer membrane usher protein FimD, plug domain	CATH (4.3.0)
E	2.60.40.2070	Mainly Beta	Sandwich	Immunoglobulin-like	PapC, C-terminal domain	CATH (4.3.0)
B	3.10.20.410	Alpha Beta	Roll	Ubiquitin-like (UB roll)	PapC, N-terminal domain	CATH (4.3.0)
B	2.60.40.3110	Mainly Beta	Sandwich	Immunoglobulin-like	Outer membrane usher protein	CATH (4.3.0)
B	2.60.40.2610	Mainly Beta	Sandwich	Immunoglobulin-like	Outer membrane usher protein FimD, plug domain	CATH (4.3.0)
B	2.60.40.2070	Mainly Beta	Sandwich	Immunoglobulin-like	PapC, C-terminal domain	CATH (4.3.0)
D	2.60.40.1090	Mainly Beta	Sandwich	Immunoglobulin-like	Fimbrial-type adhesion domain	CATH (4.3.0)
A	2.60.40.1090	Mainly Beta	Sandwich	Immunoglobulin-like	Fimbrial-type adhesion domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF02753	Pili assembly chaperone PapD, C-terminal domain (PapD_C)	Pili assembly chaperone PapD, C-terminal domain	Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD.	Domain
C, F	PF00345	Pili and flagellar-assembly chaperone, PapD N-terminal domain (PapD_N)	Pili and flagellar-assembly chaperone, PapD N-terminal domain	C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly.	Domain
B, E	PF13953	PapC C-terminal domain (PapC_C)	PapC C-terminal domain	The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents th ...	The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologues. This domain has a beta-sandwich structure similar to the plug domain of PapC [1].	Domain
B, E	PF00577	Outer membrane usher protein (Usher)	Outer membrane usher protein	-	Family
A, D	PF00419	Fimbrial protein (Fimbrial)	Fimbrial protein		Domain
A, D	PF09160	FimH, mannose binding (FimH_man-bind)	FimH, mannose binding	Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology. They are predominantly found in bacterial mannose-specific adhesins, since they are capable of binding ...	Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology. They are predominantly found in bacterial mannose-specific adhesins, since they are capable of binding to D-mannose [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Chaperone protein fimC	protein folding chaperone	protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization	cellular anatomical structure outer membrane-bounded periplasmic space cell envelope periplasmic space
B, E	Outer membrane usher protein, type 1 fimbrial synthesis	wide pore channel activity passive transmembrane transporter activity channel activity porin activity fimbrial usher porin activity transporter activity transmembrane transporter activity	cellular component biogenesis cellular component organization cellular component assembly cell projection organization cellular process pilus assembly cellular component organization or biogenesis pilus organization cell projection assembly	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
A, D	Type 1 fimbrial adhesin	binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding	cell adhesion cellular process behavior multicellular organismal process response to stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus mechanosensory behavior cell-substrate adhesion cell adhesion involved in biofilm formation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms cell adhesion cellular process behavior multicellular organismal process response to stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus mechanosensory behavior cell-substrate adhesion cell adhesion involved in biofilm formation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation cell adhesion involved in single-species biofilm formation single-species submerged biofilm formation	pilus cell projection cellular anatomical structure pilus tip host cellular component host cell part host cell membrane other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR036316	Pili assembly chaperone, C-terminal domain superfamily	Homologous Superfamily
C, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, F	IPR050643	Periplasmic Pilus Chaperone	Family
C, F	IPR016148	Pili assembly chaperone, C-terminal	Domain
C, F	IPR008962	PapD-like superfamily	Homologous Superfamily
C, F	IPR016147	Pili assembly chaperone, N-terminal	Domain
C, F	IPR001829	Pili assembly chaperone, bacterial	Family
C, F	IPR018046	Pili assembly chaperone, conserved site	Conserved Site
B, E	IPR042186	Outer membrane usher protein FimD, plug domain	Homologous Superfamily
B, E	IPR037224	PapC, N-terminal domain superfamily	Homologous Superfamily
B, E	IPR018030	Fimbrial membrane usher, conserved site	Conserved Site
B, E	IPR025885	PapC, N-terminal domain	Domain
B, E	IPR043142	PapC-like, C-terminal domain superfamily	Homologous Superfamily
B, E	IPR025949	PapC-like, C-terminal domain	Domain
B, E	IPR000015	Outer membrane usher protein	Family
A, D	IPR036937	Fimbrial-type adhesion domain superfamily	Homologous Superfamily
A, D	IPR015243	FimH, mannose-binding domain	Domain
A, D	IPR050263	Bacterial Fimbrial Adherence	Family
A, D	IPR000259	Fimbrial-type adhesion domain	Domain
A, D	IPR008966	Adhesion domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	OPM	Transmembrane	Beta-barrel transmembrane	Fimbrial usher porin (n=24,S=26)	Fimbrial usher porin

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Beta-Barrel Membrane Proteins: Monomeric/Dimeric	P pilus FimD usher bound to FimC:FimH substrate