6QZF

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)
A [auth 0a]	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)
C [auth 0c]	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)
H [auth 0h]	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)
K [auth 0k]	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)
E [auth 0e]	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)
I [auth 0i]	SCOP2B Superfamily	Upper collar protein gp10 (connector protein)	8036294	3001932	SCOP2B (2022-06-29)
L [auth 0l]	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)
A [auth 0a]	Phage_connector_1st	e6qzf0a1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
A [auth 0a]	Phage_connector_2nd	e6qzf0a2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
B [auth 0b]	Phage_connector_1st	e6qzf0b2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
B [auth 0b]	Phage_connector_2nd	e6qzf0b1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
C [auth 0c]	Phage_connector_1st	e6qzf0c2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
C [auth 0c]	Phage_connector_2nd	e6qzf0c1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
G [auth 0g]	Phage_connector_1st	e6qzf0g1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
G [auth 0g]	Phage_connector_2nd	e6qzf0g2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
H [auth 0h]	Phage_connector_1st	e6qzf0h1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
H [auth 0h]	Phage_connector_2nd	e6qzf0h2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
J [auth 0j]	Phage_connector_1st	e6qzf0j2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
J [auth 0j]	Phage_connector_2nd	e6qzf0j1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
K [auth 0k]	Phage_connector_1st	e6qzf0k2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
K [auth 0k]	Phage_connector_2nd	e6qzf0k1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
D [auth 0d]	Phage_connector_1st	e6qzf0d2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
D [auth 0d]	Phage_connector_2nd	e6qzf0d1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
E [auth 0e]	Phage_connector_1st	e6qzf0e1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
E [auth 0e]	Phage_connector_2nd	e6qzf0e2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
F [auth 0f]	Phage_connector_1st	e6qzf0f2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
F [auth 0f]	Phage_connector_2nd	e6qzf0f1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
I [auth 0i]	Phage_connector_1st	e6qzf0i2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
I [auth 0i]	Phage_connector_2nd	e6qzf0i1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)
L [auth 0l]	Phage_connector_1st	e6qzf0l2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: Phage_connector_1st	ECOD (1.6)
L [auth 0l]	Phage_connector_2nd	e6qzf0l1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: Phage_connector_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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]	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
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 organic cyclic compound 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
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
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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms viral life cycle symbiont-mediated disruption of host cell envelope biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell via disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical entity symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell receptor-mediated virion attachment to host cell symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms viral life cycle symbiont-mediated disruption of host cell envelope biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell via disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical entity symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell	virus tail, fiber virus tail virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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	Pectate lyase superfamily protein	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

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6QZF

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

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