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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION NMR STRUCTURE OF THE MITOCHONDRIAL PROTEIN IMPORT RECEPTOR TOM20 FROM RAT IN A COMPLEX WITH A PRESEQUENCE PEPTIDE DERIVED FROM RAT ALDEHYDE DEHYDROGENASE (ALDH)

Authors :   Y. Abe, T. Shodai, T. Muto, K. Mihara, H. Torii, S. Nishikawa, T. Endo, D. Kohda

Date :   23 Apr 99 (Deposition) - 02 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Mitochondrial Protein Import Across Outer Membrane, Receptor For Presequences, Mitochondrial Targeting Signal, Presequence Peptide, Receptor/Oxidoreductase Complex Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Abe, T. Shodai, T. Muto, K. Mihara, H. Torii, S. Nishikawa, T. Endo, D. Kohda
Structural Basis Of Presequence Recognition By The Mitochondrial Protein Import Receptor Tom20.
Cell(Cambridge, Mass. ) V. 100 551 2000
PubMed-ID: 10721992 | Reference-DOI: 10.1016/S0092-8674(00)80691-1
(for further references see the PDB file header)

Molecule 1 - PROTEIN (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20)
	Cellular Location	:	MITOCHONDRIAL OUTER MEMBRANE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 51-145
	Organelle	:	MITOCHONDRIA
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	CYTOSOLIC DOMAIN, LIMITED PROTEOLYZED FRAGMENT

Molecule 2 - PROTEIN (MITOCHONDRIAL ALDEHYDE DEHYDROGENASE)
	Chains	:	B
	EC Number	:	1.2.1.3
	Engineered	:	YES
	Fragment	:	RESIDUES 12-22
	Mutation	:	YES
	Other Details	:	C-TERMINAL HALF OF THE PRESEQUENCE OF MITOCHONDRIAL PRECURSOR
	Other Details - Source	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATUALLY FOUND IN RATTUS NORVEGICUS (RAT). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN BL21(DE3), PLASMID PET-17XB.
	Synonym	:	ALDH
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1OM2)

(no "Site" information available for 1OM2)

(no "SS Bond" information available for 1OM2)

(no "Cis Peptide Bond" information available for 1OM2)

(no "SAP(SNP)/Variant" information available for 1OM2)

(no "PROSITE Motif" information available for 1OM2)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000027088	1	ENSRNOE00000194302	chr19:56863167-56862937	231	TOM20_RAT	1-41	41	0	-	-
1.2	ENSRNOT00000027088	2	ENSRNOE00000194357	chr19:56859134-56859088	47	TOM20_RAT	41-56	16	1	A:1-6	6
1.3	ENSRNOT00000027088	3	ENSRNOE00000194378	chr19:56857774-56857693	82	TOM20_RAT	57-84	28	1	A:7-34	28
1.4	ENSRNOT00000027088	4	ENSRNOE00000344303	chr19:56852725-56852583	143	TOM20_RAT	84-131	48	1	A:34-81	48
1.5	ENSRNOT00000027088	5	ENSRNOE00000194431	chr19:56851327-56850851	477	TOM20_RAT	132-145	14	1	A:82-95	14

NMR Structure

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

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	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:95
 aligned with TOM20_RAT | Q62760 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:95
                                    60        70        80        90       100       110       120       130       140     
            TOM20_RAT    51 RAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLAEDDVE 145
               SCOP domains d1om2a_ A: Mitochondrial import receptor subunit Tom20                                          SCOP domains
               CATH domains 1om2A00 A:1-95  [code=1.20.960.10, no name defined]                                             CATH domains
               Pfam domains MAS20-1om2A0----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhh...hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2   Exon 1.3  PDB: A:7-34       -----------------------------------------------Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: A:34-81 UniProt: 84-131          -------------- Transcript 1 (2)
                 1om2 A   1 RAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLGEDDVE  95
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with ALDH2_RAT | P11884 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:11
                                    21 
            ALDH2_RAT    12 GPRLSRLLSAA  22
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1om2 B   1 GPRLSRLLSYA  11
                                    10

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 '\|'

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Mitochondrial Import Receptor Subunit Tom20; Chain A (25)

Homologous Superfamily: [code=1.20.960.10, no name defined] (1)

Norway rat (Rattus norvegicus) (1)

1om2A00

A:1-95

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MAS20] (3)

Family: MAS20 (3)

Rattus norvegicus (Rat) (3)

MAS20-1om2A01

A:1-12

NMR Structure(hide GO term definitions)

Chain A (TOM20_RAT | Q62760)

molecular function
	GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
	GO:0030943	mitochondrion targeting sequence binding	Interacting selectively and non-covalently with a mitochondrion targeting sequence, a specific peptide sequence that acts as a signal to localize the protein within the mitochondrion.
	GO:0015266	protein channel activity	Enables the energy-independent facilitated diffusion, mediated by passage of proteins through a transmembrane aqueous pore or channel.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	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:0070096	mitochondrial outer membrane translocase complex assembly	The aggregation, arrangement and bonding together of a set of components to form a mitochondrial outer membrane translocase complex.
	GO:0030150	protein import into mitochondrial matrix	The import of proteins across the outer and inner mitochondrial membranes into the matrix. Unfolded proteins enter the mitochondrial matrix with a chaperone protein; the information required to target the precursor protein from the cytosol to the mitochondrial matrix is contained within its N-terminal matrix-targeting sequence. Translocation of precursors to the matrix occurs at the rare sites where the outer and inner membranes are close together.
	GO:0006605	protein targeting	The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
	GO:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
	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:0016031	tRNA import into mitochondrion	The directed movement of tRNA, transfer ribonucleic acid, from the cytoplasm into a mitochondrion.
	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:0044233	ER-mitochondrion membrane contact site	A zone of apposition between endoplasmic-reticulum and mitochondrial membranes, structured by bridging complexes. These contact sites are thought to facilitate inter-organelle calcium and phospholipid exchange.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031307	integral component of mitochondrial outer membrane	The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005740	mitochondrial envelope	The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005742	mitochondrial outer membrane translocase complex	A large complex of the mitochondrial outer membrane that mediates transport of proteins into all mitochondrial compartments.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B (ALDH2_RAT | P11884)

molecular function
	GO:0070404	NADH binding	Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0004029	aldehyde dehydrogenase (NAD) activity	Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + H+.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	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:0071398	cellular response to fatty acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
	GO:0032870	cellular response to hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0006068	ethanol catabolic process	The chemical reactions and pathways resulting in the breakdown of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0055093	response to hyperoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0035094	response to nicotine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nicotine stimulus.
	GO:0032570	response to progesterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

NMR Structure
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