Domain Annotation: SCOP Classification SCOP Database (version: 2.0) Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species
A	d4need_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ]
B	d4neel_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ]
C	d4neef_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ]
D	d4neei_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ]
I	d4neee1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
I	d4neee2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
J	d4neeh1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
J	d4neeh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
K	d4neek1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
K	d4neek2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
L	d4neec1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]
L	d4neec2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ]

Domain Annotation: CATH CATH Database (version 4.2.0) Homepage

Chain	Domain	Class	Architecture	Topology	Homology
A	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase
B	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase
C	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase
D	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase
E	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant
F	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant
G	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant
H	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant
I	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor
J	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor
K	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor
L	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, B, C, D	PF01217	Clathrin adaptor complex small chain (Clat_adaptor_s)	Clathrin adaptor complex small chain	-	Domain
E, F, G, H	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Family
E, F, G, H	PF02296	Alpha adaptin AP2, C-terminal domain (Alpha_adaptin_C)	Alpha adaptin AP2, C-terminal domain	-	Family
E, F, G, H	PF02883	Adaptin C-terminal domain (Alpha_adaptinC2)	Adaptin C-terminal domain	Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and ...	Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins.	Domain
I, J, K, L	PF00469	Negative factor, (F-Protein) or Nef (F-protein)	Negative factor, (F-Protein) or Nef	-	Family

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F, I, L	AP-2 complex subunit sigma	binding protein binding clathrin binding protein-macromolecule adaptor activity clathrin adaptor activity molecular adaptor activity cargo adaptor activity		intracellular anatomical structure cytoplasm plasma membrane clathrin-coated pit endomembrane system vesicle membrane membrane membrane coat clathrin coat AP-type membrane coat adaptor complex vesicle coat AP-2 adaptor complex clathrin vesicle coat clathrin coat of endocytic vesicle clathrin adaptor complex clathrin coat of coated pit coated vesicle clathrin-coated vesicle endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane clathrin-coated vesicle membrane endocytic vesicle membrane clathrin-coated endocytic vesicle membrane organelle membrane cytoplasmic vesicle vesicle protein-containing complex organelle membrane-bounded organelle clathrin-coated endocytic vesicle coated membrane cell periphery intracellular vesicle bounding membrane of organelle plasma membrane region membrane protein complex plasma membrane protein complex cellular anatomical entity intracellular organelle intracellular membrane-bounded organelle
A, B, G, J	AP-2 complex subunit alpha-2	protein-macromolecule adaptor activity molecular adaptor activity cargo adaptor activity binding protein binding clathrin binding clathrin adaptor activity protein domain specific binding disordered domain specific binding enzyme binding kinase binding phospholipid binding lipid binding phosphatidylinositol binding protein kinase binding protein-containing complex binding		intracellular anatomical structure cytoplasm plasma membrane clathrin-coated pit endomembrane system vesicle membrane membrane membrane coat clathrin coat AP-type membrane coat adaptor complex vesicle coat AP-2 adaptor complex clathrin vesicle coat clathrin coat of endocytic vesicle clathrin adaptor complex clathrin coat of coated pit coated vesicle clathrin-coated vesicle endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane clathrin-coated vesicle membrane endocytic vesicle membrane clathrin-coated endocytic vesicle membrane organelle membrane cytoplasmic vesicle vesicle protein-containing complex organelle membrane-bounded organelle clathrin-coated endocytic vesicle coated membrane cell periphery intracellular vesicle bounding membrane of organelle plasma membrane region membrane protein complex plasma membrane protein complex cellular anatomical entity synaptic vesicle cell junction transport vesicle synapse exocytic vesicle presynapse secretory vesicle
C, E, H, K	Protein Nef	binding protein binding SH3 domain binding protein domain specific binding	cellular process viral process cellular component organization viral life cycle fusion of virus membrane with host plasma membrane membrane fusion involved in viral entry into host cell biological process involved in symbiotic interaction entry into host biological process involved in interspecies interaction between organisms multi-organism cellular process multi-organism membrane fusion multi-organism membrane organization viral entry into host cell biological process involved in interaction with host multi-organism process movement in host environment membrane organization membrane fusion cellular component organization or biogenesis pathogenesis regulation of defense response to virus by virus uncoating of virus virion assembly	extracellular region cellular anatomical entity host cellular component host cell cytoplasm host cell part host cell membrane host cell endomembrane system host intracellular part host cell cytoplasm part host intracellular region host cell host cell Golgi apparatus host cell Golgi membrane host cell plasma membrane membrane virion

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.