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Title :   VHS DOMAIN OF TOM1 PROTEIN FROM H. SAPIENS

Authors :   S. Misra, B. Beach, J. H. Hurley

Date :   13 Mar 00 (Deposition) - 22 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Superhelix Of Helices, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Misra, B. Beach, J. H. Hurley
Structure Of The Vhs Domain Of Human Tom1 (Target Of Myb 1): Insights Into Interactions With Proteins And Membranes
Biochemistry V. 39 11282 2000
PubMed-ID: 10985773 | Reference-DOI: 10.1021/BI0013546
(for further references see the PDB file header)

Molecule 1 - TARGET OF MYB1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	VHS DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ELK)

(no "Site" information available for 1ELK)

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

(no "Cis Peptide Bond" information available for 1ELK)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053845	R	84	H	TOM1_HUMAN	Polymorphism	11558473	A/B	R	84	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053845	R	84	H	TOM1_HUMAN	Polymorphism	11558473	A	R	84	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_053845	R	84	H	TOM1_HUMAN	Polymorphism	11558473	B	R	84	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VHS	PS50179	VHS domain profile.	TOM1_HUMAN	20-152	2	A:20-152 B:20-152

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VHS	PS50179	VHS domain profile.	TOM1_HUMAN	20-152	1	A:20-152 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VHS	PS50179	VHS domain profile.	TOM1_HUMAN	20-152	1	- B:20-152

(no "Exon" information available for 1ELK)

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:153
 aligned with TOM1_HUMAN | O60784 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           TOM1_HUMAN     1 MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPM 153
               SCOP domains d1elka_ A: Tom1 protein                                                                                                                                   SCOP domains
               CATH domains 1elkA00 A:1-153  [code=1.25.40.90, no name defined]                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------H--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------VHS  PDB: A:20-152 UniProt: 20-152                                                                                                   - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1elk A   1 SDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPM 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with TOM1_HUMAN | O60784 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           TOM1_HUMAN     1 MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPM 153
               SCOP domains d1elkb_ B: Tom1 protein                                                                                                                                   SCOP domains
               CATH domains 1elkB00 B:1-153  [code=1.25.40.90, no name defined]                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------H--------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------VHS  PDB: B:20-152 UniProt: 20-152                                                                                                   - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1elk B   1 SDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPM 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ENTH/VHS domain (36)

Family: VHS domain (16)

Protein domain: Tom1 protein (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1elka_	A:
1b	d1elkb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Alpha Horseshoe (399)

Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat (320)

Homologous Superfamily: [code=1.25.40.90, no name defined] (33)

Human (Homo sapiens) (20)

1a	1elkA00	A:1-153
1b	1elkB00	B:1-153

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (TOM1_HUMAN | O60784)

molecular function
	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).
biological process
	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:0016197	endosomal transport	The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
	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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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