2VYI - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TPR DOMAIN OF HUMAN SGT

Authors :   S. Dutta, Y. J. Tan

Date :   24 Jul 08 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Sgt, Chaperone, Tpr Repeat, Phosphoprotein, Tetratricopeptide Repeat Protein, Host-Virus Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dutta, Y. J. Tan
Structural And Functional Characterization Of Human Sgt And Its Interaction With Vpu Of The Human Immunodeficiency Virus Type 1.
Biochemistry V. 47 10123 2008
PubMed-ID: 18759457 | Reference-DOI: 10.1021/BI800758A

Molecule 1 - SGTA PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	TETRATRICOPEPTIDE REPEAT, RESIDUES 84-210
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEAT 1, SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT (TPR)-CONTAINING, ALPHA, ISOFORM CRA_A

		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 2VYI)

(no "Site" information available for 2VYI)

(no "SS Bond" information available for 2VYI)

(no "Cis Peptide Bond" information available for 2VYI)

(no "SAP(SNP)/Variant" information available for 2VYI)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	SGTA_HUMAN	91-124 125-158 159-192	6	A:91-124 B:91-124 A:125-158 B:125-158 A:159-192 B:159-192
2	TPR_REGION	PS50293	TPR repeat region circular profile.	SGTA_HUMAN	91-192	2	A:91-192 B:91-192

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	SGTA_HUMAN	91-124 125-158 159-192	3	A:91-124 - A:125-158 - A:159-192 -
2	TPR_REGION	PS50293	TPR repeat region circular profile.	SGTA_HUMAN	91-192	1	A:91-192 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPR	PS50005	TPR repeat profile.	SGTA_HUMAN	91-124 125-158 159-192	3	- B:91-124 - B:125-158 - B:159-192
2	TPR_REGION	PS50293	TPR repeat region circular profile.	SGTA_HUMAN	91-192	1	- B:91-192

(no "Exon" information available for 2VYI)

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:128
 aligned with SGTA_HUMAN | O43765 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:134
                                    86        96       106       116       126       136       146       156       166       176       186       196       206    
           SGTA_HUMAN    77 SPARTPPSEEDSAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREAP 210
               SCOP domains d2v      yia_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------TPR  PDB: A:91-124 UniProt: 91-124TPR  PDB: A:125-158               TPR  PDB: A:159-192               ------------------ PROSITE (1)
                PROSITE (2) --------------TPR_REGION  PDB: A:91-192 UniProt: 91-192                                                             ------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vyi A  80 GPL------EDSAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREAP 210
                              |     86        96       106       116       126       136       146       156       166       176       186       196       206    
                             82     86

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SGTA_HUMAN | O43765 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:124
                                    95       105       115       125       135       145       155       165       175       185       195       205    
           SGTA_HUMAN    86 EDSAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA 209
               SCOP domains d2vyib_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------TPR_1-2vyiB01 B:159-192           ----------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------TPR_1-2vyiB02 B:159-192           ----------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------TPR_1-2vyiB03 B:159-192           ----------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------TPR_1-2vyiB04 B:159-192           ----------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------TPR_1-2vyiB05 B:159-192           ----------------- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------TPR_1-2vyiB06 B:159-192           ----------------- Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TPR  PDB: B:91-124 UniProt: 91-124TPR  PDB: B:125-158               TPR  PDB: B:159-192               ----------------- PROSITE (1)
                PROSITE (2) -----TPR_REGION  PDB: B:91-192 UniProt: 91-192                                                             ----------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vyi B  86 EDSAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA 209
                                    95       105       115       125       135       145       155       165       175       185       195       205

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: TPR-like (83)

Family: Tetratricopeptide repeat (TPR) (47)

Protein domain: automated matches (11)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d2vyia_	A:
1b	d2vyib_	B:

(no "CATH Domain" information available for 2VYI)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TPR (230)

Family: TPR_1 (18)

Homo sapiens (Human) (11)

1a	TPR_1-2vyiB01	B:159-192
1b	TPR_1-2vyiB02	B:159-192
1c	TPR_1-2vyiB03	B:159-192
1d	TPR_1-2vyiB04	B:159-192
1e	TPR_1-2vyiB05	B:159-192
1f	TPR_1-2vyiB06	B:159-192

Asymmetric Unit(hide GO term definitions)

Chain A,B (SGTA_HUMAN | O43765)

molecular function
	GO:1904288	BAT3 complex binding	Interacting selectively and non-covalently with a BAT3 complex.
	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:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:1903071	positive regulation of ER-associated ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of ER-associated ubiquitin-dependent protein catabolic 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.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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Biological Units
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	2vyi
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	SGTA_HUMAN \| O43765	:	4cpg 4god 4goe 4gof

(no "Related Entries Specified in the PDB File" available for 2VYI)

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Ligands, Modified Residues, Ions (0, 0)

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