4YTX | pdb_00004ytx

Crystal structure of Ups1-Mdm35 complex with PA

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bet v1-like	8095907	3000738	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Endosomal sorting complex assembly domain-like	8095908	3000610	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)
P	PRELI	e4ytxP1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
N	PRELI	e4ytxN1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
L	PRELI	e4ytxL1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
J	PRELI	e4ytxJ1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
H	PRELI	e4ytxH1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
F	PRELI	e4ytxF1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
D	PRELI	e4ytxD1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
B	PRELI	e4ytxB1	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PRELI	ECOD (1.6)
O	UPF0203	e4ytxO1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
M	UPF0203	e4ytxM1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
K	UPF0203	e4ytxK1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
I	UPF0203	e4ytxI1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
G	UPF0203	e4ytxG1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
E	UPF0203	e4ytxE1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
C	UPF0203	e4ytxC1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)
A	UPF0203	e4ytxA1	A: alpha bundles	X: Mitochondrial distribution and morphology protein 35 (From Topology)	H: Mitochondrial distribution and morphology protein 35 (From Topology)	T: Mitochondrial distribution and morphology protein 35	F: UPF0203	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N, P	PF04707	PRELI-like family (PRELI)	PRELI-like family	-	Family
A, C, E, G, I A, C, E, G, I, K, M, O	PF05254	Uncharacterised protein family (UPF0203) (UPF0203)	Uncharacterised protein family (UPF0203)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	Protein UPS1, mitochondrial	phospholipid transfer activity lipid transporter activity lipid transfer activity phosphatidic acid transfer activity transporter activity phospholipid transporter activity binding lipid binding	localization transport macromolecule localization phospholipid transport lipid localization lipid transport establishment of localization organophosphate ester transport phosphatidylglycerol metabolic process glycerophospholipid metabolic process primary metabolic process cardiolipin metabolic process phospholipid metabolic process organophosphate metabolic process localization transport macromolecule localization phospholipid transport lipid localization lipid transport establishment of localization organophosphate ester transport phosphatidylglycerol metabolic process glycerophospholipid metabolic process primary metabolic process cardiolipin metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerolipid metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process regulation of cellular process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of phosphatidylcholine biosynthetic process positive regulation of lipid metabolic process phosphatidylcholine metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process positive regulation of phosphorus metabolic process glycerophospholipid biosynthetic process biological regulation regulation of phosphatidylcholine metabolic process positive regulation of phospholipid biosynthetic process regulation of phospholipid metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process positive regulation of phospholipid metabolic process biosynthetic process positive regulation of lipid biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process regulation of phosphorus metabolic process regulation of lipid biosynthetic process phosphatidylcholine biosynthetic process regulation of metabolic process regulation of phosphatidylcholine biosynthetic process membrane organization phospholipid translocation lipid translocation regulation of membrane lipid distribution cellular component organization cellular component organization or biogenesis regulation of biological quality	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle lumen
A, C, E, G, I A, C, E, G, I, K, M, O	Mitochondrial distribution and morphology protein 35	-	localization transport macromolecule localization phospholipid transport lipid localization lipid transport establishment of localization organophosphate ester transport cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex organization localization transport macromolecule localization phospholipid transport lipid localization lipid transport establishment of localization organophosphate ester transport cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis mitochondrion organization membrane organization intermembrane lipid transfer phospholipid translocation biological regulation lipid translocation regulation of membrane lipid distribution regulation of biological quality	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen mitochondrial envelope nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR006797	PRELI/MSF1 domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR037365	Slowmo/Ups family	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR007918	Mitochondrial distribution/morphology family 35/apoptosis	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B, D, F, H, J B, D, F, H, J, L, N, P	OPM	Monotopic/peripheral	Alpha + Beta monotopic/peripheral	PRELI/MSF1	UPS1 transporter

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.