1PDP | pdb_00001pdp

Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
R	d1pdpr_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
Q	d1pdpq_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
P	d1pdpp_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
O	d1pdpo_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
N	d1pdpn_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
M	d1pdpm_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
L	d1pdpl_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
K	d1pdpk_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
J	d1pdpj_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
I	d1pdpi_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
H	d1pdph_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
G	d1pdpg_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
F	d1pdpf_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
E	d1pdpe_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
D	d1pdpd_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
C	d1pdpc_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
B	d1pdpb_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1pdpa_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
R	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	gp9	8041251	3000227	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	gp9	8041251	3000227	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)
R	DHDPS	e1pdpR1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
Q	DHDPS	e1pdpQ1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
P	DHDPS	e1pdpP1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
O	DHDPS	e1pdpO1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
N	DHDPS	e1pdpN1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
M	DHDPS	e1pdpM1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
L	DHDPS	e1pdpL1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
K	DHDPS	e1pdpK1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
J	DHDPS	e1pdpJ1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
I	DHDPS	e1pdpI1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
H	DHDPS	e1pdpH1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
G	DHDPS	e1pdpG1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
F	DHDPS	e1pdpF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
E	DHDPS	e1pdpE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
D	DHDPS	e1pdpD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
C	DHDPS	e1pdpC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
B	DHDPS	e1pdpB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)
A	DHDPS	e1pdpA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DHDPS	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF07880	Bacteriophage T4 gp9/10-like protein, N-terminal (T4_gp9_10_N)	Bacteriophage T4 gp9/10-like protein, N-terminal	This entry represents the N-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment t ...	This entry represents the N-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich. This entry represents the region including these two domains. Noticeably, the long flexible region between N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres [2]. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF23618	Bacteriophage T4 gp9/10-like protein, C-terminal (T4_gp9_10_C)	Bacteriophage T4 gp9/10-like protein, C-terminal	This entry represents the C-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment t ...	This entry represents the C-terminal domain of Baseplate protein gp9 from Bacteriophage T4, a component of the viral baseplate [1]. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The C-terminal domain is thought to be essential for trimerisation and is organised into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins [2]. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate [1].	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, H, I, J, K, L, M, N, O, P, Q, R	Baseplate structural protein Gp9	-	exit from host cell biological process involved in interspecies interaction between organisms viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion assembly viral tail assembly	virus tail virion component virus tail, baseplate

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR036240	Gp9-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR008987	Baseplate structural protein Gp9/Gp10, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR027412	Baseplate structural protein Gp9 C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR056391	Baseplate protein gp9-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR027411	Baseplate structural protein Gp9/Gp10 middle domain superfamily	Homologous Superfamily

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.