4AYF | pdb_00004ayf

Crystal structure of the complex of the Caf1M:Caf1 chaperone:subunit preassembly complex carrying the Tyr40Ala mutation in the Caf1M chaperone

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ayfa1	All beta proteins	Immunoglobulin-like beta-sandwich	PapD-like	Pilus chaperone	automated matches	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)
A	d4ayfa2	All beta proteins	C2 domain-like	Periplasmic chaperone C-domain	automated matches	automated matches	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)
B	d4ayfb_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Bacterial adhesins	Pilus subunits	F1 capsule antigen Caf1	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Periplasmic chaperone C-domain	8034615	3000998	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial adhesin-like	8034616	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)
A	VEGFR-1-like_Ig-like	e4ayfA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: VEGFR-1-like_Ig-like	ECOD (v294.1)
B	Avidin	e4ayfB1	A: a/b three-layered sandwiches	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: Avidin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	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
A	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
A	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	PF09255	Caf1 Capsule antigen (Antig_Caf1)	Caf1 Capsule antigen	Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the ba ...	Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CHAPERONE PROTEIN CAF1M	protein folding chaperone	cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization	cellular anatomical structure extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space
B	F1 CAPSULE ANTIGEN	-	cell adhesion cellular process	cellular anatomical structure external encapsulating structure extracellular region glycocalyx capsule pilus cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036316	Pili assembly chaperone, C-terminal domain superfamily	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR050643	Periplasmic Pilus Chaperone	Family
A	IPR016148	Pili assembly chaperone, C-terminal	Domain
A	IPR008962	PapD-like superfamily	Homologous Superfamily
A	IPR016147	Pili assembly chaperone, N-terminal	Domain
A	IPR001829	Pili assembly chaperone, bacterial	Family
A	IPR018046	Pili assembly chaperone, conserved site	Conserved Site
B	IPR036937	Fimbrial-type adhesion domain superfamily	Homologous Superfamily
B	IPR015335	F1 capsule antigen	Family
B	IPR008966	Adhesion domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.