6VYK | pdb_00006vyk

Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs

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)
A	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8037798	3000496	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8037796	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Mechanosensitive channel protein MscS (YggB), transmembrane region	8037799	3000754	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	MS_channel_2nd	e6vykA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
A	MS_channel_1st	e6vykA3	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
A	MS_channel_3rd	e6vykA2	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
B	MS_channel_2nd	e6vykB3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
B	MS_channel_1st	e6vykB2	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
B	MS_channel_3rd	e6vykB1	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
C	MS_channel_2nd	e6vykC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
C	MS_channel_1st	e6vykC2	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
C	MS_channel_3rd	e6vykC3	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
D	MS_channel_2nd	e6vykD3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
D	MS_channel_1st	e6vykD1	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
D	MS_channel_3rd	e6vykD2	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
E	MS_channel_2nd	e6vykE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
E	MS_channel_1st	e6vykE3	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
E	MS_channel_3rd	e6vykE2	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
F	MS_channel_2nd	e6vykF2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
F	MS_channel_1st	e6vykF3	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
F	MS_channel_3rd	e6vykF1	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)
G	MS_channel_2nd	e6vykG3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MS_channel_2nd	ECOD (1.6)
G	MS_channel_1st	e6vykG1	A: alpha bundles	X: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	H: Mechanosensitive channel protein MscS (YggB), transmembrane region (From Topology)	T: Mechanosensitive channel protein MscS (YggB), transmembrane region	F: MS_channel_1st	ECOD (1.6)
G	MS_channel_3rd	e6vykG2	A: a+b two layers	X: Alpha-beta plaits	H: Mechanosensitive channel protein MscS (YggB), C-terminal domain (From Topology)	T: Mechanosensitive channel protein MscS (YggB), C-terminal domain	F: MS_channel_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
A	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
A	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
A	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
B	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
B	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
B	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
C	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
C	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
C	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
D	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
D	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
D	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
E	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
E	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
E	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
F	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
F	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
F	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)
G	1.10.287.1260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	CATH (utative)
G	2.30.30.60	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
G	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF05552	Mechanosensitive ion channel, conserved TM helix (MS_channel_1st_1)	Mechanosensitive ion channel, conserved TM helix	-	Family
A, B, C, D, E A, B, C, D, E, F, G	PF00924	Mechanosensitive ion channel, beta-domain (MS_channel_2nd)	Mechanosensitive ion channel, beta-domain	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antipara ...	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet (middle/second) domain and a C-terminal alpha/beta-domain [4-7]. This is the beta domain which adopts a SH3-like barrel structure.	Domain
A, B, C, D, E A, B, C, D, E, F, G	PF21088	Mechanosensitive ion channel, transmembrane helices 2/3 (MS_channel_1st)	Mechanosensitive ion channel, transmembrane helices 2/3	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antipara ...	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet (middle/second) domain and a C-terminal alpha/beta-domain [4-7]. The N-terminal region consists of three membrane spanning helices (TM1, TM2 and TM3), TM2 and TM3 are represented in this entry. In the heptamer, the permeation pathway is formed by the packing of TM3s, flanked by TM1-TM2 helical hairpins [4].	Domain
A, B, C, D, E A, B, C, D, E, F, G	PF21082	Mechanosensitive ion channel MscS, C-terminal (MS_channel_3rd)	Mechanosensitive ion channel MscS, C-terminal	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antipara ...	This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet domain (beta-domain, Pfam:PF00924) and a C-terminal alpha/beta-domain [1,2,3]. This is the C-terminal domain of McsS which, together with the middle beta-domain, creates a framework that connects to the cytoplasm through distinct openings [4-6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G	Mechanosensitive channel MscS	identical protein binding protein binding binding 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	transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis regulation of cellular component size homeostatic process cell volume homeostasis biological regulation cellular homeostasis intracellular water homeostasis chemical homeostasis intracellular chemical homeostasis regulation of biological quality regulation of cell size regulation of anatomical structure size	cellular anatomical structure membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR006685	Mechanosensitive ion channel MscS	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR011014	Mechanosensitive ion channel MscS, transmembrane-2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR008910	Mechanosensitive ion channel, conserved TM helix	Repeat
A, B, C, D, E A, B, C, D, E, F, G	IPR011066	Mechanosensitive ion channel MscS, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR023408	Mechanosensitive ion channel MscS, beta-domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR049142	Mechanosensitive ion channel, transmembrane helices 2/3	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR006686	Mechanosensitive ion channel MscS, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G	IPR049278	Mechanosensitive ion channel MscS, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR045275	Mechanosensitive ion channel MscS, archaea/bacteria type	Family

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, G	OPM	Transmembrane	Alpha-helical polytopic	Small conductance mechanosensitive ion channel (MscS)	Small conductance mechanosensitive ion channels

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G	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, G	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, G	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Mechanosensitive	MscS voltage-modulated mechanosensitive channel in PC-18:1 nanodiscs