6OXL

CRYO-EM STRUCTURE OF PHOSPHORYLATED AP-2 (mu E302K) BOUND TO NECAP IN THE PRESENCE OF SS DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Clathrin adaptor core protein	8093671	4001978	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ARM repeat-like	8093672	3000116	SCOP2 (2022-06-29)
D [auth S]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
E [auth N]	SCOP2 Family	Necap1 N-terminal domain-like	8094486	4001928	SCOP2 (2022-06-29)
E [auth N]	SCOP2 Superfamily	PH domain-like	8094487	3000134	SCOP2 (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	Adaptin_N	e6oxlA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
B	Adaptin_N	e6oxlB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
C [auth M]	Adap_comp_sub_2nd	e6oxlM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Adap_comp_sub_2nd	ECOD (1.6)
C [auth M]	Adap_comp_sub_1st	e6oxlM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Adap_comp_sub_1st	ECOD (1.6)
C [auth M]	Clat_adaptor_s	e6oxlM3	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
D [auth S]	Clat_adaptor_s	e6oxlS1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
E [auth N]	DUF1681	e6oxlN1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: DUF1681	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)
C [auth M]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (utative)
C [auth M]	2.60.40.1170	Mainly Beta	Sandwich	Immunoglobulin-like	Mu homology domain, subdomain B	CATH (utative)
D [auth S]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Repeat
B	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Repeat
C [auth M]	PF01217	Clathrin adaptor complex small chain (Clat_adaptor_s)	Clathrin adaptor complex small chain	-	Domain
C [auth M]	PF00928	Adaptor complexes medium subunit family (Adap_comp_sub)	Adaptor complexes medium subunit family	-	Family
D [auth S]	PF01217	Clathrin adaptor complex small chain (Clat_adaptor_s)	Clathrin adaptor complex small chain	-	Domain
E [auth N]	PF07933	Protein of unknown function (DUF1681) (DUF1681)	Protein of unknown function (DUF1681)	This family is composed of sequences derived from a number of hypothetical eukaryotic proteins of unknown function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	AP-2 complex subunit alpha-2	binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding kinase binding enzyme binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding kinase binding enzyme binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor activity disordered domain specific binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process hemopoiesis biological regulation cell development regulation of cell differentiation regulation of hematopoietic stem cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation anatomical structure development hematopoietic stem cell differentiation developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process hemopoiesis biological regulation cell development regulation of cell differentiation regulation of hematopoietic stem cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation anatomical structure development hematopoietic stem cell differentiation cellular process regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation localization import into cell transport clathrin-dependent endocytosis receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular localization receptor internalization postsynaptic neurotransmitter receptor internalization vesicle-mediated transport in synapse protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis establishment of localization in cell regulation of biological quality protein localization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport	membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle protein-containing complex vesicle coat membrane protein complex membrane coat cell periphery bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex membrane plasma membrane coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane organelle membrane clathrin adaptor complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane postsynapse synapse cell junction transport vesicle presynapse synaptic vesicle exocytic vesicle
B	AP-2 complex subunit beta	clathrin binding protein binding binding protein-containing complex binding	developmental process heart development multicellular organism development multicellular organismal process cardiac septum development cardiac chamber development anatomical structure development animal organ development circulatory system development system development synaptic vesicle endocytosis import into cell cellular localization transport developmental process heart development multicellular organism development multicellular organismal process cardiac septum development cardiac chamber development anatomical structure development animal organ development circulatory system development system development synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis ventricular septum development cardiac ventricle development artery development aorta development vasculature development blood vessel development clathrin-dependent endocytosis receptor-mediated endocytosis receptor internalization postsynaptic neurotransmitter receptor internalization biological regulation protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality protein localization regulation of localization regulation of biological process regulation of cellular process regulation of protein localization positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane regulation of cellular localization cellular macromolecule localization macromolecule localization positive regulation of protein localization regulation of protein localization to membrane positive regulation of cellular process establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport intracellular protein transport clathrin coat assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis coronary vasculature development kidney development renal system development positive regulation of cellular component organization regulation of cellular component organization regulation of transport regulation of vesicle-mediated transport positive regulation of endocytosis positive regulation of transport regulation of endocytosis	protein-containing complex intracellular anatomical structure membrane membrane protein complex cellular anatomical entity coated membrane clathrin coat membrane coat AP-type membrane coat adaptor complex cytoplasm clathrin adaptor complex membrane-bounded organelle vesicle coat intracellular vesicle protein-containing complex intracellular anatomical structure membrane membrane protein complex cellular anatomical entity coated membrane clathrin coat membrane coat AP-type membrane coat adaptor complex cytoplasm clathrin adaptor complex membrane-bounded organelle vesicle coat intracellular vesicle endomembrane system intracellular organelle cell periphery bounding membrane of organelle AP-2 adaptor complex cytoplasmic vesicle vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex plasma membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle organelle membrane synapse cell junction glutamatergic synapse extrinsic component of plasma membrane presynaptic endocytic zone presynaptic membrane extrinsic component of presynaptic endocytic zone membrane synaptic membrane extrinsic component of synaptic membrane presynapse presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane postsynapse
C [auth M]	AP-2 complex subunit mu	signal sequence binding binding peptide binding protein binding transmembrane transporter binding lipid binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding disordered domain specific binding signal sequence binding binding peptide binding protein binding transmembrane transporter binding lipid binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding disordered domain specific binding protein domain specific binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell endocytosis protein localization regulation of localization regulation of cellular process regulation of protein localization negative regulation of biological process negative regulation of protein localization to plasma membrane cellular macromolecule localization negative regulation of cellular process regulation of protein localization to membrane negative regulation of protein localization regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation localization within membrane regulation of protein localization to cell periphery protein localization to membrane negative regulation of protein localization to membrane regulation of cellular localization macromolecule localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane receptor internalization receptor-mediated endocytosis regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process regulation of receptor internalization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of receptor internalization positive regulation of transport clathrin-dependent endocytosis postsynaptic neurotransmitter receptor internalization protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality regulation of cellular component size regulation of vesicle size regulation of anatomical structure size membrane organization vesicle budding from membrane vesicle organization organelle organization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport intracellular protein transport positive regulation of synaptic vesicle recycling regulation of synaptic vesicle recycling regulation of synaptic vesicle endocytosis positive regulation of synaptic vesicle endocytosis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle clathrin-coated pit membrane endomembrane system cell periphery plasma membrane intracellular vesicle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle clathrin-coated pit membrane endomembrane system cell periphery plasma membrane intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle protein-containing complex vesicle coat membrane protein complex membrane coat bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane organelle membrane clathrin adaptor complex synapse cell junction glutamatergic synapse extrinsic component of plasma membrane presynaptic endocytic zone presynaptic membrane extrinsic component of presynaptic endocytic zone membrane synaptic membrane extrinsic component of synaptic membrane presynapse presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane postsynapse
D [auth S]	AP-2 complex subunit sigma	cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport synaptic vesicle endocytosis import into cell synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling endocytosis clathrin-dependent endocytosis receptor-mediated endocytosis receptor internalization postsynaptic neurotransmitter receptor internalization biological regulation protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality	synapse cell junction cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle synapse cell junction cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle membrane protein complex endomembrane system membrane coat bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex cytoplasmic vesicle vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane cytoplasm organelle membrane clathrin adaptor complex postsynapse glutamatergic synapse extrinsic component of plasma membrane presynaptic endocytic zone presynaptic membrane extrinsic component of presynaptic endocytic zone membrane synaptic membrane extrinsic component of synaptic membrane presynapse presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane
E [auth N]	Adaptin ear-binding coat-associated protein 2	-	localization transport cellular process establishment of localization vesicle-mediated transport import into cell endocytosis protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization localization transport cellular process establishment of localization vesicle-mediated transport import into cell endocytosis protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization	cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex membrane coat intracellular organelle bounding membrane of organelle vesicle membrane cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex membrane coat intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle clathrin-coated vesicle clathrin vesicle coat coated vesicle vesicle clathrin-coated vesicle membrane coated membrane intracellular membrane-bounded organelle clathrin coat coated vesicle membrane cytoplasmic vesicle membrane organelle cytoplasm organelle membrane
F [auth n]	Unknown region of Adaptin ear-binding coat-associated protein 2 Ex-domain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR003164	Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain	Domain
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR012295	TBP domain superfamily	Homologous Superfamily
A	IPR002553	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Domain
A	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
A	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
A	IPR017104	Adaptor protein complex AP-2, alpha subunit	Family
A	IPR009028	Coatomer/calthrin adaptor appendage, C-terminal subdomain	Homologous Superfamily
B	IPR016024	Armadillo-type fold	Homologous Superfamily
B	IPR013037	Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain	Homologous Superfamily
B	IPR000225	Armadillo	Repeat
B	IPR026739	AP complex subunit beta	Family
B	IPR011989	Armadillo-like helical	Homologous Superfamily
B	IPR012295	TBP domain superfamily	Homologous Superfamily
B	IPR002553	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Domain
B	IPR015151	Beta-adaptin appendage, C-terminal subdomain	Domain
B	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
B	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
B	IPR009028	Coatomer/calthrin adaptor appendage, C-terminal subdomain	Homologous Superfamily
B	IPR016342	AP-1/2/4 complex subunit beta	Family
C [auth M]	IPR043512	Mu2, C-terminal domain	Domain
C [auth M]	IPR036168	AP-2 complex subunit mu, C-terminal superfamily	Homologous Superfamily
C [auth M]	IPR028565	Mu homology domain	Domain
C [auth M]	IPR018240	Clathrin adaptor, mu subunit, conserved site	Conserved Site
C [auth M]	IPR001392	Clathrin adaptor, mu subunit	Family
C [auth M]	IPR011012	Longin-like domain superfamily	Homologous Superfamily
C [auth M]	IPR043532	AP-2 complex subunit mu, N-terminal	Domain
C [auth M]	IPR022775	AP complex, mu/sigma subunit	Domain
D [auth S]	IPR016635	Adaptor protein complex, sigma subunit	Family
D [auth S]	IPR011012	Longin-like domain superfamily	Homologous Superfamily
D [auth S]	IPR000804	Clathrin adaptor complex, small chain	Conserved Site
D [auth S]	IPR022775	AP complex, mu/sigma subunit	Domain
D [auth S]	IPR027156	AP-2 complex subunit sigma	Family
E [auth N]	IPR012466	NECAP, PHear domain	Domain
E [auth N]	IPR011993	PH-like domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth M]	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047
F [auth n]	UNK	RESID: AA0038