Annotations: 3J31

Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
R [auth P]	MR_MLE_N	e3j31P1	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: MR_MLE_N	ECOD (v295.2)
Q [auth O]	Peptidase_M10	e3j31O1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
Q [auth O]	N6_Mtase	e3j31O2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
P [auth N]	HypA	e3j31N1	A: alpha arrays	X: Lipocalins/Streptavidin	H: Enterocin 7A and 7B	T: Enterocin 7A and 7B	F: HypA	ECOD (v295.2)
O [auth M]	Peptidase_M10	e3j31M1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
O [auth M]	N6_Mtase	e3j31M2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
N [auth L]	Peptidase_M10	e3j31L1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
N [auth L]	N6_Mtase	e3j31L2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
M [auth K]	Peptidase_M10	e3j31K1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
M [auth K]	N6_Mtase	e3j31K2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
L [auth J]	Peptidase_M10	e3j31J1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
L [auth J]	N6_Mtase	e3j31J2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
K [auth I]	Peptidase_M10	e3j31I1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
K [auth I]	N6_Mtase	e3j31I2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
J [auth H]	Peptidase_M10	e3j31H1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
J [auth H]	N6_Mtase	e3j31H2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
I [auth G]	Peptidase_M10	e3j31G1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
I [auth G]	N6_Mtase	e3j31G2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
H [auth F]	Peptidase_M10	e3j31F1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
H [auth F]	N6_Mtase	e3j31F2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
G [auth E]	Peptidase_M10	e3j31E1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
G [auth E]	N6_Mtase	e3j31E2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
F [auth D]	Peptidase_M10	e3j31D1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
F [auth D]	N6_Mtase	e3j31D2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
E [auth C]	Peptidase_M10	e3j31C1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
E [auth C]	N6_Mtase	e3j31C2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
D [auth B]	Peptidase_M10	e3j31B1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
D [auth B]	N6_Mtase	e3j31B2	A: alpha arrays	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: N6_Mtase	ECOD (v295.2)
C [auth A]		e3j31A1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v295.2)
C [auth A]	SusG_C	e3j31A2	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SusG_C	ECOD (v295.2)
A [auth Q]	STIV_penton_2nd	e3j31Q1	A: alpha arrays	X: TIM beta/alpha-barrel	H: NTF2-like	T: NTF2-like	F: STIV_penton_2nd	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
R [auth P]	PF21879	C381 turret protein Nucleoplasmin-like/VP domain (STIV_turret_3rd)	C381 turret protein Nucleoplasmin-like/VP domain	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein third jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions o ...	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein third jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions.	Domain
R [auth P]	PF21878	C381 turret protein 1st galactose-binding domain-like (STIV_turret_1st)	C381 turret protein 1st galactose-binding domain-like	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein first jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions o ...	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein first jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions [1].	Domain
R [auth P]	PF21876	C381 turret protein 2nd galactose-binding domain-like (STIV_turret_2nd)	C381 turret protein 2nd galactose-binding domain-like	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein second jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions ...	This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein second jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions.	Domain
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O]	PF22405	Sulfolobus turreted icosahedral virus 1-like, major capsid protein (STIV-like_capsid)	Sulfolobus turreted icosahedral virus 1-like, major capsid protein	This entry represents a jelly-roll domain present in the major capsid protein from Sulfolobus turreted icosahedral virus 1. The structure of this domain is similar to major capsid protein structures of the eukaryotic Paramecium bursaria Chlorella vir ...	This entry represents a jelly-roll domain present in the major capsid protein from Sulfolobus turreted icosahedral virus 1. The structure of this domain is similar to major capsid protein structures of the eukaryotic Paramecium bursaria Chlorella virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenovirus [1,2].	Domain
A [auth Q]	PF21881	A223 penton protein second domain (STIV_penton_2nd)	A223 penton protein second domain	This Pfam entry represents the Sulfolobus turreted icosahedral virus (STIV) penton protein second jelly roll domain. STIV is a virus that infects the archaeon Sulfolobus solfataricus and was isolated in acidic hot springs. The virus has a unique arch ...	This Pfam entry represents the Sulfolobus turreted icosahedral virus (STIV) penton protein second jelly roll domain. STIV is a virus that infects the archaeon Sulfolobus solfataricus and was isolated in acidic hot springs. The virus has a unique architecture based on a pseudo T = 31d capsid symmetry with each icosahedral asymmetric unit consisting of 15 copies of the coat subunit (B345), one copy of the A223 penton base protein, one copy of the C381 turret protein, and one copy of the A55 membrane protein. The pentameric penton base protein is a crucial component of the virus as it forms the vertices of the capsid shell and decorates the penton base structure forming the first floor of the turret. The penton protein contains three different layers, with the N termini forming a 10-stranded beta-pore, the middle layer comprising a canonical viral jelly-roll forming a pentameric ring, and the C-terminal forming a second pentameric ring of jelly-rolls. The virus shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. The conservation of the A223 penton base jelly-roll fold, as well as the B345 double jelly-roll fold, strongly suggests an evolutionary connection for these protein modules among phages, archaeal viruses, and eukaryotic viruses.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
R [auth P]	C381 turret protein	-	-	-
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O]	Coat protein	-	-	viral capsid virion component
B [auth R]	A55 membrane protein	-	-	-
A [auth Q]	A223 penton base	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
R [auth P]	IPR054072	C381 turret protein, N-terminal	Domain
R [auth P]	IPR054073	C381 turret protein, C-terminal	Domain
R [auth P]	IPR054070	C381 turret protein, middle domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O]	IPR055085	Major capsid protein, jelly-roll	Domain
A [auth Q]	IPR054074	A223 penton protein, C-terminal	Domain

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.

3J31 | pdb_00003j31

Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage