6QZF | pdb_00006qzf

The cryo-EM structure of the collar complex and tail axis in genome emptied bacteriophage phi29

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth 0l]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
K [auth 0k]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
J [auth 0j]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
I [auth 0i]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
H [auth 0h]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
G [auth 0g]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
F [auth 0f]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
E [auth 0e]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
D [auth 0d]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
C [auth 0c]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
B [auth 0b]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
A [auth 0a]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	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)
L [auth 0l]	DAO	e6qzf0l1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
K [auth 0k]	DAO	e6qzf0k1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
J [auth 0j]	DAO	e6qzf0j1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
I [auth 0i]	DAO	e6qzf0i1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
H [auth 0h]	DAO	e6qzf0h1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
G [auth 0g]	DAO	e6qzf0g1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
F [auth 0f]	DAO	e6qzf0f1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
E [auth 0e]	DAO	e6qzf0e1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
D [auth 0d]	DAO	e6qzf0d1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
C [auth 0c]	DAO	e6qzf0c1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
B [auth 0b]	DAO	e6qzf0b1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)
A [auth 0a]	DAO	e6qzf0a1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M [auth 0A], N [auth 0B], O [auth 0C], P [auth 0D], Q [auth 0E], M [auth 0A], N [auth 0B], O [auth 0C], P [auth 0D], Q [auth 0E], R [auth 0F], S [auth 0G], T [auth 0H], U [auth 0I], V [auth 0J], W [auth 0K], X [auth 0L]	PF05352	Phage Connector (GP10) (Phage_connector)	Phage Connector (GP10)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	Pre-neck appendage protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell envelope virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell envelope symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism	virus tail, fiber virus tail virion component
M [auth 0A], N [auth 0B], O [auth 0C], P [auth 0D], Q [auth 0E], M [auth 0A], N [auth 0B], O [auth 0C], P [auth 0D], Q [auth 0E], R [auth 0F], S [auth 0G], T [auth 0H], U [auth 0I], V [auth 0J], W [auth 0K], X [auth 0L]	Proximal tail tube connector protein	-	symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host symbiont genome ejection through host cell envelope, short tail mechanism viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	virus tail, tube virus tail virion component
A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], F [auth 0f], G [auth 0g], H [auth 0h], I [auth 0i], J [auth 0j], K [auth 0k], L [auth 0l]	Portal protein	RNA binding binding nucleic acid binding	virion assembly viral process viral life cycle viral genome packaging viral DNA genome packaging symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host symbiont genome ejection through host cell envelope, short tail mechanism biological process involved in interaction with host biological process involved in symbiotic interaction	viral procapsid virion component protein-containing complex viral capsid viral portal complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	IPR006626	Parallel beta-helix repeat	Repeat
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	IPR012334	Pectin lyase fold	Homologous Superfamily
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	IPR021865	Peptidase G2, IMC autoproteolytic cleavage domain	Domain
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	IPR024535	Rhamnogalacturonase A/B/Epimerase-like, pectate lyase domain	Domain
AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], AA [auth C], AB [auth c], BA [auth D], BB [auth d], CA [auth E], CB [auth e], DA [auth F], DB [auth f], EA [auth G], EB [auth g], FA [auth H], FB [auth h], GA [auth I], GB [auth i], HA [auth J], HB [auth j], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], WA [auth Y], XA [auth Z], Y [auth A], YA [auth a], Z [auth B], ZA [auth b]	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily
A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], F [auth 0f], G [auth 0g], H [auth 0h], I [auth 0i], J [auth 0j], K [auth 0k], L [auth 0l]	IPR008016	Portal protein Gp10	Family
A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], A [auth 0a], B [auth 0b], C [auth 0c], D [auth 0d], E [auth 0e], F [auth 0f], G [auth 0g], H [auth 0h], I [auth 0i], J [auth 0j], K [auth 0k], L [auth 0l]	IPR036199	Portal protein Gp10 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.