3P9H - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE TSG101 UEV DOMAIN IN COMPLEX WITH FA258 PEPTIDE

Authors :   J. H. Hurley, Y. J. Im

Date :   17 Oct 10 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein Transport, Ubiquitin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Kim, F. Liu, Y. J. Im, A. G. Stephen, M. J. Fivash, A. A. Waheed, E. O. Freed, R. J. Fisher, J. H. Hurley, T. R. Burke
Elucidation Of New Binding Interactions With The Tumor Susceptibility Gene 101 (Tsg101) Protein Using Modified Hiv-1 Gag-P6 Derived Peptide Ligands.
Acs Med Chem Lett V. 2 337 2011
PubMed-ID: 21643473 | Reference-DOI: 10.1021/ML1002579

Molecule 1 - TUMOR SUSCEPTIBILITY GENE 101 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGST2
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL UEV DOMAIN (UNP RESIDUES 2 TO 145)
	Gene	:	TSG101
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ESCRT-I COMPLEX SUBUNIT TSG101

Molecule 2 - GAG POLYPROTEIN
	Chains	:	B
	Engineered	:	YES
	Fragment	:	MODIFIED HIV-1 GAG PTAP MOTIF
	Other Details	:	PEPTIDE (PEPTAPPEE) WITH MODIFIED PROLINE 3 BY TRANS- 4-(3,4-DIMETHOXYBENZYL OXIME) GROUP
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	ZYJ	1	Mod. Amino Acid	(4R)-4-({[(1E)-(3,4-DIMETHOXYPHENYL)METHYLIDENE]AMINO}OXY)-L-PROLINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:6 , THR A:56 , THR A:58 , ASN A:69 , PRO A:71 , LYS A:90 , THR A:92 , GLU B:2 , THR B:4	BINDING SITE FOR RESIDUE ZYJ B 3

(no "SS Bond" information available for 3P9H)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:80	-	Pro A:81
2	His A:119	-	Pro A:120

(no "SAP(SNP)/Variant" information available for 3P9H)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UEV	PS51322	UEV domain profile.	TS101_HUMAN	2-145	1	A:2-145

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000251968	1a	ENSE00001129196	chr11:18548489-18548322	168	TS101_HUMAN	1-14	14	1	A:1-14	14
1.2	ENST00000251968	2	ENSE00001106778	chr11:18541150-18541066	85	TS101_HUMAN	15-43	29	1	A:15-43	29
1.3	ENST00000251968	3	ENSE00001615198	chr11:18537711-18537646	66	TS101_HUMAN	43-65	23	1	A:43-65 (gaps)	23
1.4	ENST00000251968	4	ENSE00001604894	chr11:18536388-18536225	164	TS101_HUMAN	65-119	55	1	A:65-119	55
1.5	ENST00000251968	5	ENSE00001631564	chr11:18531212-18531089	124	TS101_HUMAN	120-161	42	1	A:120-145	26
1.6	ENST00000251968	6	ENSE00001601359	chr11:18528470-18528404	67	TS101_HUMAN	161-183	23	0	-	-
1.7b	ENST00000251968	7b	ENSE00001106774	chr11:18524124-18524033	92	TS101_HUMAN	183-214	32	0	-	-
1.8	ENST00000251968	8	ENSE00001106772	chr11:18505619-18505417	203	TS101_HUMAN	214-281	68	0	-	-
1.9	ENST00000251968	9	ENSE00001106782	chr11:18503416-18503177	240	TS101_HUMAN	282-361	80	0	-	-
1.10a	ENST00000251968	10a	ENSE00001106781	chr11:18502182-18501862	321	TS101_HUMAN	362-390	29	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:141
 aligned with TS101_HUMAN | Q99816 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
          TS101_HUMAN     1 MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP 145
               SCOP domains d3p9ha_ A: Tumor susceptibility gene 101 (T    SG101)                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------UEV-3p9hA01 A:21-141                                                                                                     ---- Pfam domains
         Sec.struct. author ...hhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeeeeh----hheeeeeeeeeeeeee..eeeeeeeeeee.........eeee.....eee.............hhhhhh......hhhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UEV  PDB: A:2-145 UniProt: 2-145                                                                                                                 PROSITE
           Transcript 1 (1) Exon 1.1a     Exon 1.2  PDB: A:15-43       ---------------------Exon 1.4  PDB: A:65-119 UniProt: 65-119                Exon 1.5  PDB: A:120-145   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3 UniProt: 43-65-------------------------------------------------------------------------------- Transcript 1 (2)
                 3p9h A   1 SAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYG----GSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP 145
                                    10        20        30        40  |    |50        60        70        80        90       100       110       120       130       140     
                                                                     43   48

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with Q9YP46_9HIV1 | Q9YP46 from UniProtKB/TrEMBL  Length:500

    Alignment length:11
                                   461 
         Q9YP46_9HIV1   452 RPEPTAPPEES 462
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains -Gag_p6-3p- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3p9h B   0 xPEpTAPPEEx  10
                            |  |     9|
                            |  |     10-NH2
                            0-ACE      
                               3-ZYJ

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	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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: UEV domain (15)

Protein domain: Tumor susceptibility gene 101 (TSG101) (11)

Human (Homo sapiens) [TaxId: 9606] (11)

d3p9ha_

(no "CATH Domain" information available for 3P9H)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: UBC (69)

Family: UEV (11)

Homo sapiens (Human) (8)

UEV-3p9hA01

A:21-141

Clan: no clan defined [family: Gag_p6] (6)

Family: Gag_p6 (6)

Human immunodeficiency virus 1 (4)

Gag_p6-3p9hB01

B:1-9

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TS101_HUMAN | Q99816)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0046790	virion binding	Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
biological process
	GO:0097352	autophagosome maturation	Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	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:0008333	endosome to lysosome transport	The directed movement of substances from endosomes to lysosomes.
	GO:0075733	intracellular transport of virus	The directed movement of a virus, or part of a virus, within the host cell.
	GO:0030216	keratinocyte differentiation	The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
	GO:0036258	multivesicular body assembly	The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:1903543	positive regulation of exosomal secretion	Any process that activates or increases the frequency, rate or extent of exosomal secretion.
	GO:2000397	positive regulation of ubiquitin-dependent endocytosis	Any process that activates or increases the frequency, rate or extent of ubiquitin-dependent endocytosis.
	GO:1903774	positive regulation of viral budding via host ESCRT complex	Any process that activates or increases the frequency, rate or extent of viral budding via host ESCRT complex.
	GO:0048524	positive regulation of viral process	Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
	GO:1902188	positive regulation of viral release from host cell	Any process that activates or increases the frequency, rate or extent of viral release from host cell.
	GO:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a 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:0043405	regulation of MAP kinase activity	Any process that modulates the frequency, rate or extent of MAP kinase activity.
	GO:0001558	regulation of cell growth	Any process that modulates the frequency, rate, extent or direction of cell growth.
	GO:1903551	regulation of extracellular exosome assembly	Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.
	GO:0040008	regulation of growth	Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
	GO:1903772	regulation of viral budding via host ESCRT complex	Any process that modulates the frequency, rate or extent of viral budding via host ESCRT complex.
	GO:1902186	regulation of viral release from host cell	Any process that modulates the frequency, rate or extent of viral release from host cell.
	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:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
	GO:0046755	viral budding	A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
	GO:0039702	viral budding via host ESCRT complex	Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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:0000813	ESCRT I complex	An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated cargoes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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 B (Q9YP46_9HIV1 | Q9YP46)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0046755	viral budding	A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
	GO:0039702	viral budding via host ESCRT complex	Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
	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.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019013	viral nucleocapsid	The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric/Biological Unit
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	3p9h
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	TS101_HUMAN \| Q99816
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UniProtKB/Swiss-Prot
	Q9YP46_9HIV1 \| Q9YP46	:	2l45 2l46 3oua 3ouc 3p9g
	TS101_HUMAN \| Q99816	:	1kpp 1kpq 1m4p 1m4q 1s1q 2f0r 3iv1 3obq 3obs 3obu 3obx 3p9g 4eje 4yc1 4zny
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	Q9YP46_9HIV1 \| Q9YP46	:	2l44 4ep3 4epj 4eq0 4fae

Description

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Ligands, Modified Residues, Ions (3, 3)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (5, 5)

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