1JJ7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL ATPASE DOMAIN OF HUMAN TAP1

Authors :   R. Gaudet, D. C. Wiley

Date :   03 Jul 01 (Deposition) - 12 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   P-Loop, Abc Atpase Domain, Helical Domain, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Gaudet, D. C. Wiley
Structure Of The Abc Atpase Domain Of Human Tap1, The Transporter Associated With Antigen Processing.
Embo J. V. 20 4964 2001
PubMed-ID: 11532960 | Reference-DOI: 10.1093/EMBOJ/20.17.4964
(for further references see the PDB file header)

Molecule 1 - PEPTIDE TRANSPORTER TAP1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL ABC ATPASE DOMAIN
	Gene	:	TAP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:36 , HOH A:40 , HOH A:46 , HOH A:61 , SER A:545 , ADP A:752	BINDING SITE FOR RESIDUE MG A 902
2	AC2	SOFTWARE	HOH A:4 , HOH A:7 , HOH A:13 , HOH A:19 , HOH A:33 , HOH A:36 , HOH A:40 , HOH A:46 , HOH A:62 , HOH A:82 , HOH A:103 , TYR A:512 , ARG A:515 , VAL A:520 , PRO A:539 , ASN A:540 , GLY A:541 , SER A:542 , GLY A:543 , LYS A:544 , SER A:545 , THR A:546 , THR A:613 , VAL A:617 , MG A:902	BINDING SITE FOR RESIDUE ADP A 752

(no "SS Bond" information available for 1JJ7)

(no "Cis Peptide Bond" information available for 1JJ7)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013153	V	578	I	TAP1_HUMAN	Polymorphism	41561219	A	V	518	I
2	UniProt	VAR_000093	D	697	G	TAP1_HUMAN	Polymorphism	1135216	A	D	637	G
3	UniProt	VAR_013154	R	708	Q	TAP1_HUMAN	Polymorphism	1057149	A	R	648	Q
4	UniProt	VAR_013173	R	719	Q	TAP1_HUMAN	Unclassified	121917702	A	R	659	Q
5	UniProt	VAR_047514	Q	768	R	TAP1_HUMAN	Polymorphism	1057149	A	Q	708	R

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	TAP1_HUMAN	703-717	1	A:643-657

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.43	ENST00000383235	43	ENSE00001770017	HSCHR6_MHC_QBL:32750465-32749526	940	TAP1_HUMAN	1-260	260	0	-	-
1.44a	ENST00000383235	44a	ENSE00001803544	HSCHR6_MHC_QBL:32748989-32748875	115	TAP1_HUMAN	260-298	39	0	-	-
1.45	ENST00000383235	45	ENSE00001769567	HSCHR6_MHC_QBL:32748726-32748596	131	TAP1_HUMAN	298-342	45	0	-	-
1.46	ENST00000383235	46	ENSE00001697273	HSCHR6_MHC_QBL:32747636-32747431	206	TAP1_HUMAN	342-410	69	0	-	-
1.47	ENST00000383235	47	ENSE00001623480	HSCHR6_MHC_QBL:32747004-32746807	198	TAP1_HUMAN	411-476	66	0	-	-
1.48b	ENST00000383235	48b	ENSE00001801886	HSCHR6_MHC_QBL:32745605-32745477	129	TAP1_HUMAN	477-519	43	0	-	-
1.48c	ENST00000383235	48c	ENSE00001704906	HSCHR6_MHC_QBL:32745327-32745139	189	TAP1_HUMAN	520-582	63	1	A:492-522	31
1.49b	ENST00000383235	49b	ENSE00001741941	HSCHR6_MHC_QBL:32744579-32744406	174	TAP1_HUMAN	583-640	58	1	A:523-580	58
1.50a	ENST00000383235	50a	ENSE00001782977	HSCHR6_MHC_QBL:32744162-32744000	163	TAP1_HUMAN	641-695	55	1	A:581-635	55
1.50d	ENST00000383235	50d	ENSE00001739907	HSCHR6_MHC_QBL:32743691-32743555	137	TAP1_HUMAN	695-740	46	1	A:635-680	46
1.52c	ENST00000383235	52c	ENSE00001861339	HSCHR6_MHC_QBL:32742272-32741696	577	TAP1_HUMAN	741-808	68	1	A:681-742	62

Asymmetric/Biological 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:251
 aligned with TAP1_HUMAN | Q03518 from UniProtKB/Swiss-Prot  Length:808

    Alignment length:251
                                   561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801 
           TAP1_HUMAN   552 GLLTPLHLEGLVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMVQA 802
               SCOP domains d1jj7a_ A: Peptide transporter Tap1, C-terminal ABC domain                                                                                                                                                                                                  SCOP domains
               CATH domains --------1jj7A01 A:500-740 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                           -- CATH domains
               Pfam domains -----------------------------------------------------ABC_tran-1jj7A01 A:545-671                                                                                                     ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee..........eeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhhh......hhhhhhhhhhhh.hhhhhhh..hhhhh.........hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------I----------------------------------------------------------------------------------------------------------------------G----------Q----------Q------------------------------------------------R---------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.48c  PDB: A:492-522     Exon 1.49b  PDB: A:523-580 UniProt: 583-640               Exon 1.50a  PDB: A:581-635 UniProt: 641-695            ---------------------------------------------Exon 1.52c  PDB: A:681-742 UniProt: 741-808 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.50d  PDB: A:635-680 UniProt: 695-740   -------------------------------------------------------------- Transcript 1 (2)
                 1jj7 A 492 GLLTPLHLEGLVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMVQA 742
                                   501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1jj7A01

A:500-740

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Homo sapiens (Human) (8)

ABC_tran-1jj7A01

A:545-671

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TAP1_HUMAN | Q03518)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
	GO:0042288	MHC class I protein binding	Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0023029	MHC class Ib protein binding	Interacting selectively and non-covalently with major histocompatibility complex class Ib molecules.
	GO:0042287	MHC protein binding	Interacting selectively and non-covalently with major histocompatibility complex molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0046978	TAP1 binding	Interacting selectively and non-covalently with the TAP1 subunit of TAP (transporter associated with antigen processing) protein.
	GO:0046979	TAP2 binding	Interacting selectively and non-covalently with the TAP2 subunit of TAP (transporter associated with antigen processing) protein.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
	GO:0015440	peptide-transporting ATPase activity	Catalysis of the reaction: ATP + H2O + peptide(in) = ADP + phosphate + peptide(out). Peptides exported include alpha-hemolysin, cyclolysin, colicin V and siderophores from Gram-negative bacteria, and bacteriocin, subtilin, competence factor and pediocin from Gram-positive bacteria.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0046980	tapasin binding	Interacting selectively and non-covalently with tapasin, a member of the MHC class I loading complex which bridges the TAP peptide transporter to class I molecules.
biological process
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.
	GO:0002485	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules.
	GO:0002489	antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
	GO:0002481	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent	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 Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
	GO:0046967	cytosol to ER transport	The directed movement of substances from the cytosol to the endoplasmic reticulum of a cell.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0019060	intracellular transport of viral protein in host cell	The directed movement of a viral protein within the host cell.
	GO:0015833	peptide transport	The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0002591	positive regulation of antigen processing and presentation of peptide antigen via MHC class I	Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I.
	GO:0042270	protection from natural killer cell mediated cytotoxicity	The process of protecting a cell from natural killer cell mediated cytotoxicity.
	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:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042825	TAP complex	A heterodimer composed of the subunits TAP1 and TAP2 (transporter associated with antigen presentation). Functions in the transport of antigenic peptides from the cytosol to the lumen of the endoplasmic reticulum.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0043657	host cell	A cell within a host organism. Includes the host plasma membrane and any external encapsulating structures such as the host cell wall and cell envelope.
	GO:0030176	integral component of endoplasmic reticulum membrane	The component of the endoplasmic reticulum 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: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: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: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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1JJ7)

Description

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Ligands, Modified Residues, Ions (2, 2)

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