1E42 - JenaLib

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Title :   BETA2-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2

Authors :   D. J. Owen, P. R. Evans, H. T. Mcmahon

Date :   27 Jun 00 (Deposition) - 21 Aug 00 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Endocytosis, Adaptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Owen, Y. Vallis, B. M. F. Pearse, H. T. Mcmahon, P. R. Evans
The Structure And Function Of The Beta2-Adaptin Appendage Domain
Embo J. V. 19 4216 2000
PubMed-ID: 10944104 | Reference-DOI: 10.1093/EMBOJ/19.16.4216

Molecule 1 - AP-2 COMPLEX SUBUNIT BETA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	APPENDAGE DOMAIN, RESIDUES 701-937
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT, CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN, AP105B, BETA2-ADAPTIN, ADAPTER-RELATED PROTEIN COMPLEX 2 BETA SUBUNIT, ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT BETA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	DTD	2	Ligand/Ion	DITHIANE DIOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	4	Ligand/Ion	MAGNESIUM ION
5	NI	1	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DTD	1	Ligand/Ion	DITHIANE DIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DTD	1	Ligand/Ion	DITHIANE DIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:754 , ILE A:755 , PRO A:769 , LEU A:770 , HOH A:2060	BINDING SITE FOR RESIDUE CL A 971
02	AC2	SOFTWARE	PRO A:793 , VAL A:794 , GLN B:756	BINDING SITE FOR RESIDUE CL A 972
03	AC3	SOFTWARE	ALA B:754 , ILE B:755 , PRO B:769 , LEU B:770	BINDING SITE FOR RESIDUE CL B 971
04	AC4	SOFTWARE	GLN A:756 , PRO B:793 , VAL B:794	BINDING SITE FOR RESIDUE CL B 972
05	AC5	SOFTWARE	ASN A:872 , HOH A:2198 , HOH A:2332 , HOH A:2337 , HOH A:2338 , HOH A:2340	BINDING SITE FOR RESIDUE MG A 960
06	AC6	SOFTWARE	ASN B:872 , HOH B:2225 , HOH B:2351 , HOH B:2357 , HOH B:2358 , HOH B:2361	BINDING SITE FOR RESIDUE MG B 960
07	AC7	SOFTWARE	GLU B:849 , HOH B:2253 , HOH B:2330 , HOH B:2331 , HOH B:2332 , HOH B:2389	BINDING SITE FOR RESIDUE MG B 961
08	AC8	SOFTWARE	LYS B:842 , HOH B:2199 , HOH B:2315 , HOH B:2316 , HOH B:2317 , HOH B:2325	BINDING SITE FOR RESIDUE MG B 962
09	AC9	SOFTWARE	HOH A:2096 , HOH A:2097 , HOH A:2148 , HIS B:735 , HOH B:2043 , HOH B:2049	BINDING SITE FOR RESIDUE NI B 970
10	BC1	SOFTWARE	ALA A:746 , LEU A:747 , GLN A:748 , ARG A:834 , ARG A:879 , TYR A:888 , HOH A:2067 , HOH A:2402	BINDING SITE FOR RESIDUE DTD A 950
11	BC2	SOFTWARE	ALA B:746 , LEU B:747 , GLN B:748 , ARG B:834 , ALA B:877 , ARG B:879 , TYR B:888 , HOH B:2092 , HOH B:2419	BINDING SITE FOR RESIDUE DTD B 950
12	BC3	SOFTWARE	SER A:761 , PHE A:762 , ASN A:895 , ILE A:897 , GLU A:922 , VAL A:923 , HOH A:2119	BINDING SITE FOR RESIDUE GOL A 980
13	BC4	SOFTWARE	SER B:761 , ASN B:895 , ILE B:897 , GLU B:922 , VAL B:923	BINDING SITE FOR RESIDUE GOL B 980

(no "SS Bond" information available for 1E42)

Asymmetric Unit

No.	Residues
1	Glu A:798	-	Pro A:799
2	Glu B:798	-	Pro B:799

(no "SAP(SNP)/Variant" information available for 1E42)

(no "PROSITE Motif" information available for 1E42)

(no "Exon" information available for 1E42)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:233
 aligned with AP2B1_HUMAN | P63010 from UniProtKB/Swiss-Prot  Length:937

    Alignment length:233
                                   714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934   
          AP2B1_HUMAN   705 GGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN 937
               SCOP domains d1e42a1 A:705-824 Beta2-adaptin AP2 ear domain, N-terminal subdomain                                                    d1e42a2 A:825-937 Beta2-adaptin AP2, C-terminal subdomain                                                         SCOP domains
               CATH domains 1e42A01 A:705-821  [code=2.60.40.1150, no name defined]                                                              1e42A02 A:822-937 TATA-Binding Protein                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeehhhhh..eeeeeeeeee..eeeeeeeeee.........eeee.......................eeeeeeee.............eeeeeee....eeeeeee.hhhhh.......hhhhhhhhhhhhhhhhheeeee.....hhhhhhhhhhh...eeeeeeee..eeeeeeeee.....eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e42 A 705 GGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN 937
                                   714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with AP2B1_HUMAN | P63010 from UniProtKB/Swiss-Prot  Length:937

    Alignment length:233
                                   714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934   
          AP2B1_HUMAN   705 GGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN 937
               SCOP domains d1e42b1 B:705-824 Beta2-adaptin AP2 ear domain, N-terminal subdomain                                                    d1e42b2 B:825-937 Beta2-adaptin AP2, C-terminal subdomain                                                         SCOP domains
               CATH domains 1e42B01 B:705-821  [code=2.60.40.1150, no name defined]                                                              1e42B02 B:822-937 TATA-Binding Protein                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeehhhhh..eeeeeeeeee..eeeeeeeeee.........eeee.......................eeeeeeee.............eeeeeee....eeeeeee.hhhhh.......hhhhhhhhhhhhhhhhheeeee.....hhhhhhhhhhh...eeeeeeee..eeeeeeeee.....eeeeeeee......eeeeeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e42 B 705 GGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN 937
                                   714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: TATA-Binding Protein (37)

Human (Homo sapiens) (4)

1a	1e42A02	A:822-937
1b	1e42B02	B:822-937

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1150, no name defined] (6)

Human (Homo sapiens) (4)

2a	1e42A01	A:705-821
2b	1e42B01	B:705-821

(no "Pfam Domain" information available for 1E42)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AP2B1_HUMAN | P63010)

molecular function
	GO:0035615	clathrin adaptor activity	The binding activity of a molecule that brings together clathrin and one or more other molecules, permitting them to function in a coordinated way.
	GO:0030276	clathrin binding	Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
	GO:0005048	signal sequence binding	Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
biological process
	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0035904	aorta development	The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
	GO:0003279	cardiac septum development	The progression of a cardiac septum over time, from its initial formation to the mature structure.
	GO:0048268	clathrin coat assembly	The process that results in the assembly of clathrin triskelia into the ordered structure known as a clathrin cage.
	GO:0072583	clathrin-dependent endocytosis	An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles.
	GO:0060976	coronary vasculature development	The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0007018	microtubule-based movement	A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0003281	ventricular septum development	The progression of the ventricular septum over time from its formation to the mature structure.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0030122	AP-2 adaptor complex	A heterotetrameric AP-type membrane coat adaptor complex that consists of alpha, beta2, mu2 and sigma2 subunits, and links clathrin to the membrane surface of a vesicle, and the cargo receptors during receptor/clathrin mediated endocytosis. Vesicles with AP-2-containing coats are normally found primarily near the plasma membrane, on endocytic vesicles. In at least humans, the AP-2 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different alpha genes (alphaA and alphaC).
	GO:0030131	clathrin adaptor complex	A membrane coat adaptor complex that links clathrin to a membrane.
	GO:0030118	clathrin coat	A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0005905	clathrin-coated pit	A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0036020	endolysosome membrane	The lipid bilayer surrounding an endolysosome. An endolysosome is a transient hybrid organelle formed by fusion of a late endosome with a lysosome.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030117	membrane coat	Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005802	trans-Golgi network	The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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	Cis Peptide Bonds
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	1e42
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	AP2B1_HUMAN \| P63010	:	2g30 2iv8 2iv9 2jkr 2jkt 2vgl 2xa7 4uqi 5m5r

(no "Related Entries Specified in the PDB File" available for 1E42)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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