4Y7K | pdb_00004y7k

Structure of an archaeal mechanosensitive channel in closed state

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Gated mechanosensitive channel	8100254	3000492	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Gated mechanosensitive channel	8100254	3000492	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Gated mechanosensitive channel	8100254	3000492	SCOP2B (2022-06-29)
B	SCOP2 Family	Gated mechanosensitive channel	8100253	4001874	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Gated mechanosensitive channel	8100254	3000492	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Gated mechanosensitive channel	8100254	3000492	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)
E	DMRL_synthase	e4y7kE1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
E	MscL	e4y7kE2	A: extended segments	X: Gated mechanosensitive channel (From Topology)	H: Gated mechanosensitive channel (From Topology)	T: Gated mechanosensitive channel	F: MscL	ECOD (1.6)
D	DMRL_synthase	e4y7kD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
D	MscL	e4y7kD2	A: extended segments	X: Gated mechanosensitive channel (From Topology)	H: Gated mechanosensitive channel (From Topology)	T: Gated mechanosensitive channel	F: MscL	ECOD (1.6)
C	DMRL_synthase	e4y7kC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
C	MscL	e4y7kC2	A: extended segments	X: Gated mechanosensitive channel (From Topology)	H: Gated mechanosensitive channel (From Topology)	T: Gated mechanosensitive channel	F: MscL	ECOD (1.6)
B	DMRL_synthase	e4y7kB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
B	MscL	e4y7kB2	A: extended segments	X: Gated mechanosensitive channel (From Topology)	H: Gated mechanosensitive channel (From Topology)	T: Gated mechanosensitive channel	F: MscL	ECOD (1.6)
A	DMRL_synthase	e4y7kA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
A	MscL	e4y7kA2	A: extended segments	X: Gated mechanosensitive channel (From Topology)	H: Gated mechanosensitive channel (From Topology)	T: Gated mechanosensitive channel	F: MscL	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (utative)
A	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF01741	Large-conductance mechanosensitive channel, MscL (MscL)	Large-conductance mechanosensitive channel, MscL		Domain
A, B, C, D, E	PF00885	6,7-dimethyl-8-ribityllumazine synthase (DMRL_synthase)	6,7-dimethyl-8-ribityllumazine synthase	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function f ...	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Large conductance mechanosensitive channel protein,Riboflavin synthase	riboflavin synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity passive transmembrane transporter activity gated channel activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity mechanosensitive monoatomic ion channel activity	water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process riboflavin metabolic process localization transport water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process riboflavin metabolic process localization transport monoatomic ion transport establishment of localization	protein-containing complex catalytic complex riboflavin synthase complex transferase complex cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR006399	Riboflavin synthase, archaeal	Family
A, B, C, D, E	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
A, B, C, D, E	IPR002180	Lumazine/riboflavin synthase	Family
A, B, C, D, E	IPR037673	Large-conductance mechanosensitive channel/anditomin synthesis protein L	Family
A, B, C, D, E	IPR036019	Large-conductance mechanosensitive channel MscL	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E	OPM	Transmembrane	Alpha-helical polytopic	Large conductance mechanosensitive ion channel (MscL)	Large conductance mechanosensitive ion channel (MscL)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E	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	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Mechanosensitive	MscL mechanosensitive channel in closed state

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.