4APO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   AIP TPR DOMAIN IN COMPLEX WITH HUMAN TOMM20 PEPTIDE

Authors :   R. M. L. Morgan, S. M. Roe, L. H. Pearl, C. Prodromou

Date :   04 Apr 12 (Deposition) - 23 Jan 13 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Signaling Protein-Peptide Complex, Aryl Hydrocarbon Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Morgan, L. C. Hernandez-Ramirez, G. Trivellin, L. Zhou, S. M. Roe M. Korbonits, C. Prodromou
Structure Of The Tpr Domain Of Aip: Lack Of Client Protein Interaction With The C-Terminal Alpha-7 Helix Of The Tpr Domain Of Aip Is Sufficient For Pituitary Adenoma Predisposition.
Plos One V. 7 53339 2012
PubMed-ID: 23300914 | Reference-DOI: 10.1371/JOURNAL.PONE.0053339

Molecule 1 - AH RECEPTOR-INTERACTING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTWO-E
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	TETRATRICOPEPTIDE REPEAT DOMAIN, RESIDUES 172-313
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	AIP, ARYL-HYDROCARBON RECEPTOR-INTERACTING PROTEIN, HBV X-ASSOCIATED PROTEIN 2, XAP-2, IMMUNOPHILIN HOMOLOG ARA9

Molecule 2 - MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
	Chains	:	D, E
	Fragment	:	RESIDUES 140-145
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TOMM20 C-TERMINAL PEPTIDE, MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN, OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (1x)	:	A			E
Biological Unit 2 (1x)	:		B	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	12P	1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	12P	-1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	12P	1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:203 , ILE A:206 , ALA A:207 , LYS A:210 , GLU A:249 , HIS A:253 , HOH A:2042 , HOH A:2132 , TYR B:203 , LYS B:210 , GLU B:249 , HIS B:253 , HOH B:2091 , HOH B:2241 , HOH B:2242 , HOH B:2243	BINDING SITE FOR RESIDUE 12P B1326
2	AC2	SOFTWARE	ARG B:188 , ARG B:314 , GLN B:315 , LYS B:321 , HOH B:2234 , HOH B:2246 , HOH B:2247	BINDING SITE FOR RESIDUE SO4 B1327

(no "SS Bond" information available for 4APO)

(no "Cis Peptide Bond" information available for 4APO)

Asymmetric Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043909	Q	228	K	AIP_HUMAN	Polymorphism	641081	A/B	Q	228	K
2	UniProt	VAR_043910	K	241	E	AIP_HUMAN	Unclassified	---	A/B	K	241	E
3	UniProt	VAR_043912	R	271	W	AIP_HUMAN	Unclassified	---	A/B	R	271	W
4	UniProt	VAR_043913	R	304	Q	AIP_HUMAN	Unclassified	---	A/B	R	304	Q
5	UniProt	VAR_061545	Q	307	R	AIP_HUMAN	Polymorphism	4930199	A/B	Q	307	R

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

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043909	Q	228	K	AIP_HUMAN	Polymorphism	641081	A	Q	228	K
2	UniProt	VAR_043910	K	241	E	AIP_HUMAN	Unclassified	---	A	K	241	E
3	UniProt	VAR_043912	R	271	W	AIP_HUMAN	Unclassified	---	A	R	271	W
4	UniProt	VAR_043913	R	304	Q	AIP_HUMAN	Unclassified	---	A	R	304	Q
5	UniProt	VAR_061545	Q	307	R	AIP_HUMAN	Polymorphism	4930199	A	Q	307	R

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

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043909	Q	228	K	AIP_HUMAN	Polymorphism	641081	B	Q	228	K
2	UniProt	VAR_043910	K	241	E	AIP_HUMAN	Unclassified	---	B	K	241	E
3	UniProt	VAR_043912	R	271	W	AIP_HUMAN	Unclassified	---	B	R	271	W
4	UniProt	VAR_043913	R	304	Q	AIP_HUMAN	Unclassified	---	B	R	304	Q
5	UniProt	VAR_061545	Q	307	R	AIP_HUMAN	Polymorphism	4930199	B	Q	307	R

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	AIP_HUMAN	265-298	2	A:265-298 B:265-298
2	TPR_REGION	PS50293	TPR repeat region circular profile.	AIP_HUMAN	265-298	2	A:265-298 B:265-298

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	AIP_HUMAN	265-298	1	A:265-298 -
2	TPR_REGION	PS50293	TPR repeat region circular profile.	AIP_HUMAN	265-298	1	A:265-298 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	AIP_HUMAN	265-298	1	- B:265-298
2	TPR_REGION	PS50293	TPR repeat region circular profile.	AIP_HUMAN	265-298	1	- B:265-298

(no "Exon" information available for 4APO)

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:142
 aligned with AIP_HUMAN | O00170 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:142
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311  
            AIP_HUMAN   172 DEEKAKAVPLIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQCKLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAPVVSRELQALEARI 313
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------K------------E-----------------------------W--------------------------------Q--R------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------TPR_REGION  PDB: A:265-298        --------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------TPR  PDB: A:265-298               --------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4apo A 172 AEEKAKAVPLIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQCKLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAPVVSRELQALEARI 313
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with AIP_HUMAN | O00170 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:154
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    
            AIP_HUMAN   172 DEEKAKAVPLIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQCKLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAPVVSRELQALEARIRQKDEEDKARFR 325
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------K------------E-----------------------------W--------------------------------Q--R------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------TPR_REGION  PDB: B:265-298        --------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------TPR  PDB: B:265-298               --------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4apo B 172 AEEKAKAVPLIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQCKLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAPVVSRELQALEARIRQKDEEDKARFR 325
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain D from PDB  Type:PROTEIN  Length:6
 aligned with TOM20_HUMAN | Q15388 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:6
          TOM20_HUMAN   140 AEDDVE 145
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4apo D   1 AEDDVE   6

Chain E from PDB  Type:PROTEIN  Length:6
 aligned with TOM20_HUMAN | Q15388 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:6
          TOM20_HUMAN   140 AEDDVE 145
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4apo E   1 AEDDVE   6

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

(no "SCOP Domain" information available for 4APO)

(no "CATH Domain" information available for 4APO)

(no "Pfam Domain" information available for 4APO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AIP_HUMAN | O00170)

molecular function
	GO:0036004	GAF domain binding	Interacting selectively and non-covalently with the GAF domain of a protein.
	GO:0017162	aryl hydrocarbon receptor binding	Interacting selectively and non-covalently with an aryl hydrocarbon receptor.
	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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003712	transcription cofactor activity	Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0051344	negative regulation of cyclic-nucleotide phosphodiesterase activity	Any process that stops or reduces the rate of cyclic nucleotide phosphodiesterase activity, the catalysis of the reaction: nucleotide 3',5'-cyclic phosphate + H2O = nucleotide 5'-phosphate.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0022417	protein maturation by protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
	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:1903506	regulation of nucleic acid-templated transcription	Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
	GO:0010738	regulation of protein kinase A signaling	Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006805	xenobiotic metabolic process	The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
	GO:0034751	aryl hydrocarbon receptor complex	A protein complex that acts as an aryl hydrocarbon (Ah) receptor. Cytosolic and nuclear Ah receptor complexes have different subunit composition, but both contain the ligand-binding subunit AhR.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Chain D,E (TOM20_HUMAN | Q15388)

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: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: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:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	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.

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	4apo
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	AIP_HUMAN \| O00170	:	2lkn 4aif

4aif	AIP TPR DOMAIN IN COMPLEX WITH HUMAN HSP90 PEPTIDE

Description

Compounds

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Ligands, Modified Residues, Ions (2, 2)

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