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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth Q]	F_UNCLASSIFIED	e3j31Q1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth Q]	PF21881	e3j31Q2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF21881	ECOD (1.6)
C [auth A]	F_UNCLASSIFIED	e3j31A1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth A]	PF22405	e3j31A2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
D [auth B]	F_UNCLASSIFIED	e3j31B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	PF22405	e3j31B2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
E [auth C]	F_UNCLASSIFIED	e3j31C1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth C]	PF22405	e3j31C2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
F [auth D]	F_UNCLASSIFIED	e3j31D1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth D]	PF22405	e3j31D2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
G [auth E]	F_UNCLASSIFIED	e3j31E1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth E]	PF22405	e3j31E2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
H [auth F]	F_UNCLASSIFIED	e3j31F1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
H [auth F]	PF22405	e3j31F2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
I [auth G]	F_UNCLASSIFIED	e3j31G1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
I [auth G]	PF22405	e3j31G2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
J [auth H]	F_UNCLASSIFIED	e3j31H1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth H]	PF22405	e3j31H2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
K [auth I]	F_UNCLASSIFIED	e3j31I1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth I]	PF22405	e3j31I2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
L [auth J]	F_UNCLASSIFIED	e3j31J1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
L [auth J]	PF22405	e3j31J2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
M [auth K]	F_UNCLASSIFIED	e3j31K1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
M [auth K]	PF22405	e3j31K2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
N [auth L]	F_UNCLASSIFIED	e3j31L1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
N [auth L]	PF22405	e3j31L2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
O [auth M]	F_UNCLASSIFIED	e3j31M1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
O [auth M]	PF22405	e3j31M2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
P [auth N]	F_UNCLASSIFIED	e3j31N2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
P [auth N]	PF22405	e3j31N1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
Q [auth O]	F_UNCLASSIFIED	e3j31O1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: F_UNCLASSIFIED	ECOD (1.6)
Q [auth O]	PF22405	e3j31O2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF22405	ECOD (1.6)
R [auth P]	PF21876	e3j31P1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF21876	ECOD (1.6)
R [auth P]	PF21878	e3j31P2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF21878	ECOD (1.6)
R [auth P]	PF21879	e3j31P3	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF21879	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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 vi ...	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Q]	A223 penton base	-	-	-
B [auth R]	A55 membrane 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
R [auth P]	C381 turret protein	-	-	-

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 R01GM133198.

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3J31

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