4V60 | pdb_00004v60

The structure of rat liver vault at 3.5 angstrom resolution

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)
AA [auth a]	Ribosomal_L1	e4v60a1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
AA [auth a]	Ribosomal_S18	e4v60a12	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Ribosomal_S18	ECOD (v295)
B	Ribosomal_L1	e4v60B1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
D	Ribosomal_L1	e4v60D1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
DA [auth d]	Ribosomal_L1	e4v60d1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
FA [auth f]	Ribosomal_L1	e4v60f1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
G	Ribosomal_L1	e4v60G1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
HA [auth h]	Ribosomal_L1	e4v60h1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
IA [auth i]	Ribosomal_L1	e4v60i1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
J	Ribosomal_L1	e4v60J1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
K	Ribosomal_L1	e4v60K1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
M	Ribosomal_L1	e4v60M1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
N	Ribosomal_L1	e4v60N1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
O	Ribosomal_L1	e4v60O1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
P	Ribosomal_L1	e4v60P1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
Q	Ribosomal_L1	e4v60Q1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
R	Ribosomal_L1	e4v60R1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
T	Ribosomal_L1	e4v60T1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
U	Ribosomal_L1	e4v60U1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
V	Ribosomal_L1	e4v60V1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
X	Ribosomal_L1	e4v60X1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
Y	Ribosomal_L1	e4v60Y1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
Z	Ribosomal_L1	e4v60Z1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
W	Ribosomal_L1	e4v60W1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
S	Ribosomal_L1	e4v60S1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
MA [auth m]	Ribosomal_L1	e4v60m1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
LA [auth l]	Ribosomal_L1	e4v60l1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
L	Ribosomal_L1	e4v60L1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
KA [auth k]	Ribosomal_L1	e4v60k1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
JA [auth j]	Ribosomal_L1	e4v60j1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
I	Ribosomal_L1	e4v60I1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
H	Ribosomal_L1	e4v60H1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
GA [auth g]	Ribosomal_L1	e4v60g1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
F	Ribosomal_L1	e4v60F1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
EA [auth e]	Ribosomal_L1	e4v60e1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
E	Ribosomal_L1	e4v60E1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
CA [auth c]	Ribosomal_L1	e4v60c1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
C	Ribosomal_L1	e4v60C1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
BA [auth b]	Ribosomal_L1	e4v60b1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)
A	Ribosomal_L1	e4v60A1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Ribosomal_L1	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PF01505	Major Vault Protein repeat domain (Vault)	Major Vault Protein repeat domain	The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function [1]. This family corresponds to a repeated domain found in the amino terminal half of the major vault protein.	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PF17794	Major Vault Protein repeat domain (Vault_2)	Major Vault Protein repeat domain	This short domain is found repeated numerous times in the Major Vault Protein. This entry is related to Pfam:PF01505.	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PF17795	Major Vault Protein Repeat domain (Vault_3)	Major Vault Protein Repeat domain	This domain is found in the Major Vault Protein.	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PF17796	Major Vault Protein repeat domain (Vault_4)	Major Vault Protein repeat domain		Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PF11978	Shoulder domain (MVP_shoulder)	Shoulder domain	This domain is found in the Major Vault Protein and has been called the shoulder domain [1]. This family includes two bacterial proteins Swiss:A6FXE2 and Swiss:A1ZGE7. This suggests that some bacteria may possess vault particles.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	Major vault protein	protein binding binding kinase binding enzyme binding protein kinase binding identical protein binding protein phosphatase binding phosphatase binding	cell population proliferation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction intracellular signal transduction cell communication negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process cell population proliferation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction intracellular signal transduction cell communication negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication protein activation cascade biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cytoplasm cytosol perinuclear region of cytoplasm protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cytoplasm cytosol perinuclear region of cytoplasm protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR040989	Major vault protein repeat domain 3	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR039059	Major vault protein	Family
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR041136	Major vault protein repeat domain 4	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR036013	Band 7/SPFH domain superfamily	Homologous Superfamily
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR002499	Major vault protein, N-terminal	Repeat
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR041139	Major vault protein repeat domain	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR043023	Major vault protein repeat domain superfamily	Homologous Superfamily
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR043179	Major vault protein repeat domain 2 superfamily	Homologous Superfamily
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR021870	Major vault protein, shoulder domain	Domain
A, AA [auth a], B, BA [auth b], C, A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR041134	Major vault protein repeat domain 2	Domain

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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.