5OJQ | pdb_00005ojq

The modeled structure of of wild type extended type VI secretion system sheath/tube complex in vibrio cholerae based on cryo-EM reconstruction of the non-contractile sheath/tube complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family 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)
A [auth 1]	Nrd1-Seb1_dom2	e5ojq11	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
AA [auth T]	Nrd1-Seb1_dom2	e5ojqT1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
C [auth 2]	Nrd1-Seb1_dom2	e5ojq21	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
CA [auth V]	Nrd1-Seb1_dom2	e5ojqV1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
E [auth 3]	Nrd1-Seb1_dom2	e5ojq31	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
G [auth 4]	Nrd1-Seb1_dom2	e5ojq41	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
I [auth 5]	Nrd1-Seb1_dom2	e5ojq51	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
K [auth 6]	Nrd1-Seb1_dom2	e5ojq61	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
KA [auth M]	Nrd1-Seb1_dom2	e5ojqM1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
MA [auth O]	Nrd1-Seb1_dom2	e5ojqO1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
OA [auth Q]	Nrd1-Seb1_dom2	e5ojqQ1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
QA [auth S]	Nrd1-Seb1_dom2	e5ojqS1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
S [auth L]	Nrd1-Seb1_dom2	e5ojqL1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
SA [auth U]	Nrd1-Seb1_dom2	e5ojqU1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
U [auth N]	Nrd1-Seb1_dom2	e5ojqN1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
UA [auth W]	Nrd1-Seb1_dom2	e5ojqW1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
W [auth P]	Nrd1-Seb1_dom2	e5ojqP1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
Y [auth R]	Nrd1-Seb1_dom2	e5ojqR1	A: a/b three-layered sandwiches	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (v294.1)
B [auth A]	Nop	e5ojqA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Nop	ECOD (v294.1)
M [auth a]	Nop	e5ojqa01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Nop	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], G [auth 4], I [auth 5], K [auth 6], KA [auth M], MA [auth O], OA [auth Q], QA [auth S], S [auth L], SA [auth U], U [auth N], UA [auth W], W [auth P], Y [auth R]	PF05591	Type VI secretion system, VipA, VC_A0107 or Hcp2 (T6SS_VipA)	Type VI secretion system, VipA, VC_A0107 or Hcp2	-	Family
B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], H [auth D], J [auth E], L [auth F], LA [auth Y], NA [auth b], PA [auth d], RA [auth f], T [auth X], TA [auth h], V [auth Z], VA [auth j], X [auth c], Z [auth e]	PF05943	EvpB/VC_A0108, tail sheath N-terminal domain (VipB)	EvpB/VC_A0108, tail sheath N-terminal domain	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB ...	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1].	Domain
B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], H [auth D], J [auth E], L [auth F], LA [auth Y], NA [auth b], PA [auth d], RA [auth f], T [auth X], TA [auth h], V [auth Z], VA [auth j], X [auth c], Z [auth e]	PF18945	EvpB/VC_A0108, tail sheath gpW/gp25-like domain (VipB_2)	EvpB/VC_A0108, tail sheath gpW/gp25-like domain	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/Vip ...	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1]. This entry represents the gpW/gp25-like domain.	Domain
AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], HA [auth o], IA [auth q], JA [auth s], M [auth a], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], WA [auth v], XA [auth l], YA [auth n], ZA [auth p]	PF05591	Type VI secretion system, VipA, VC_A0107 or Hcp2 (T6SS_VipA)	Type VI secretion system, VipA, VC_A0107 or Hcp2	-	Family
AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], HA [auth o], IA [auth q], JA [auth s], M [auth a], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], WA [auth v], XA [auth l], YA [auth n], ZA [auth p]	PF05943	EvpB/VC_A0108, tail sheath N-terminal domain (VipB)	EvpB/VC_A0108, tail sheath N-terminal domain	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB ...	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], G [auth 4], I [auth 5], K [auth 6], KA [auth M], MA [auth O], OA [auth Q], QA [auth S], S [auth L], SA [auth U], U [auth N], UA [auth W], W [auth P], Y [auth R]	IPR036624	Hcp1-like superfamily	Homologous Superfamily
A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], G [auth 4], I [auth 5], K [auth 6], KA [auth M], MA [auth O], OA [auth Q], QA [auth S], S [auth L], SA [auth U], U [auth N], UA [auth W], W [auth P], Y [auth R]	IPR052947	T6SS_Hcp1_domain	Unknown
A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], A [auth 1], AA [auth T], C [auth 2], CA [auth V], E [auth 3], G [auth 4], I [auth 5], K [auth 6], KA [auth M], MA [auth O], OA [auth Q], QA [auth S], S [auth L], SA [auth U], U [auth N], UA [auth W], W [auth P], Y [auth R]	IPR008514	Type VI secretion system effector Hcp	Domain
B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], H [auth D], J [auth E], L [auth F], LA [auth Y], NA [auth b], PA [auth d], RA [auth f], T [auth X], TA [auth h], V [auth Z], VA [auth j], X [auth c], Z [auth e]	IPR010269	Type VI secretion system TssC-like	Family
B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], H [auth D], J [auth E], L [auth F], LA [auth Y], NA [auth b], PA [auth d], RA [auth f], T [auth X], TA [auth h], V [auth Z], VA [auth j], X [auth c], Z [auth e]	IPR044032	TssC1, C-terminal	Domain
B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], B [auth A], BA [auth g], D [auth B], DA [auth i], F [auth C], H [auth D], J [auth E], L [auth F], LA [auth Y], NA [auth b], PA [auth d], RA [auth f], T [auth X], TA [auth h], V [auth Z], VA [auth j], X [auth c], Z [auth e]	IPR044031	TssC1, N-terminal	Domain
AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], AB [auth r], BB [auth t], EA [auth u], FA [auth k], GA [auth m], HA [auth o], IA [auth q], JA [auth s], M [auth a], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], WA [auth v], XA [auth l], YA [auth n], ZA [auth p]	IPR008312	Type VI secretion system sheath protein TssB1	Family

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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.