9QGL | pdb_00009qgl

Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state

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)
WA [auth 4A]	Integrase_Zn	e9qgl4A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Integrase_Zn	ECOD (v295.2)
ZA [auth 4D]	IBR	e9qgl4D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
YA [auth 4C]	IBR	e9qgl4C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
XA [auth 4B]	IBR	e9qgl4B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
BB [auth 4F]	IBR	e9qgl4F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
AB [auth 4E]	IBR	e9qgl4E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
RA [auth 3B]	IBR	e9qgl3B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
SA [auth 3C]	IBR	e9qgl3C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
UA [auth 3E]	IBR	e9qgl3E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
VA [auth 3F]	IBR	e9qgl3F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
TA [auth 3D]	IBR	e9qgl3D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
QA [auth 3A]	IBR	e9qgl3A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
S [auth 7A]		e9qgl7A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F:	ECOD (v295.2)
M [auth 5A]	Integrase_Zn	e9qgl5A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Integrase_Zn	ECOD (v295.2)
N [auth 5B]	IBR	e9qgl5B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
O [auth 5C]	IBR	e9qgl5C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
R [auth 5F]	IBR	e9qgl5F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
Q [auth 5E]	IBR	e9qgl5E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
P [auth 5D]	IBR	e9qgl5D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
K [auth 2E]	IBR	e9qgl2E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
L [auth 2F]	IBR	e9qgl2F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
J [auth 2D]	IBR	e9qgl2D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
I [auth 2C]	IBR	e9qgl2C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
H [auth 2B]	IBR	e9qgl2B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
G [auth 2A]	IBR	e9qgl2A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
A [auth 1A]	Integrase_Zn	e9qgl1A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Integrase_Zn	ECOD (v295.2)
B [auth 1B]	IBR	e9qgl1B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
F [auth 1F]	IBR	e9qgl1F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
E [auth 1E]	IBR	e9qgl1E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
D [auth 1D]	IBR	e9qgl1D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)
C [auth 1C]	IBR	e9qgl1C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: IBR	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], Z [auth 9B]	PF04965	Baseplate wedge protein gp25 (GPW_gp25)	Baseplate wedge protein gp25	This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to att ...	This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerisation, playing a critical role in sheath assembly and contraction [1,2]. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologues from the RpoS-mediated general stress response system (called IraD) [3,4]. This motif interacts with the 'core bundle' composed of orthologues of T4 gp6 and gp7 proteins in contractile injection systems.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], ZA [auth 4D]	Phage tail sheath family protein	-	-	-
QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], VA [auth 3F]	Phage tail sheath family protein	-	-	-
KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f]	Baseplate protein J-like domain-containing protein	-	-	-
EA [auth A], FA [auth B], GA [auth C], HA [auth D], IA [auth E], EA [auth A], FA [auth B], GA [auth C], HA [auth D], IA [auth E], JA [auth F]	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17	-	-	-
AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], Z [auth 9B]	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17	-	-	-
S [auth 7A], T [auth 7B], U [auth 7C], V [auth 7D], W [auth 7E], S [auth 7A], T [auth 7B], U [auth 7C], V [auth 7D], W [auth 7E], X [auth 7F]	Contractile injection system tube protein N-terminal domain-containing protein	-	-	-
M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], R [auth 5F]	Phage tail protein	structural molecule activity	-	-
G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], L [auth 2F]	Phage tail sheath family protein	-	-	-
A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], F [auth 1F]	Phage tail protein	structural molecule activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], ZA [auth 4D]	IPR052042	Tail sheath structural protein	Family
AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], AB [auth 4E], BB [auth 4F], WA [auth 4A], XA [auth 4B], YA [auth 4C], ZA [auth 4D]	IPR020287	Tail sheath protein, C-terminal domain	Domain
QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], VA [auth 3F]	IPR052042	Tail sheath structural protein	Family
QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], VA [auth 3F]	IPR020287	Tail sheath protein, C-terminal domain	Domain
QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], QA [auth 3A], RA [auth 3B], SA [auth 3C], TA [auth 3D], UA [auth 3E], VA [auth 3F]	IPR035089	Tail sheath protein, subtilisin-like domain	Domain
AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], AA [auth 9C], BA [auth 9D], CA [auth 9E], DA [auth 9F], Y [auth 9A], Z [auth 9B]	IPR007048	IraD/Gp25-like	Domain
S [auth 7A], T [auth 7B], U [auth 7C], V [auth 7D], W [auth 7E], S [auth 7A], T [auth 7B], U [auth 7C], V [auth 7D], W [auth 7E], X [auth 7F]	IPR045361	Contractile injection system tube protein, N-terminal domain	Domain
M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], R [auth 5F]	IPR011747	Conserved hypothetical protein CHP02241	Family
M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], M [auth 5A], N [auth 5B], O [auth 5C], P [auth 5D], Q [auth 5E], R [auth 5F]	IPR010667	Bacteriophage T4, Gp19, tail tube	Family
G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], L [auth 2F]	IPR052042	Tail sheath structural protein	Family
G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], G [auth 2A], H [auth 2B], I [auth 2C], J [auth 2D], K [auth 2E], L [auth 2F]	IPR020287	Tail sheath protein, C-terminal domain	Domain
A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], F [auth 1F]	IPR011747	Conserved hypothetical protein CHP02241	Family
A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], A [auth 1A], B [auth 1B], C [auth 1C], D [auth 1D], E [auth 1E], F [auth 1F]	IPR010667	Bacteriophage T4, Gp19, tail tube	Family

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.