3QHT - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE MONOBODY YSMB-1 BOUND TO YEAST SUMO

Authors :   S. Koide, R. N. Gilbreth

Date :   26 Jan 11 (Deposition) - 11 May 11 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Fibronectin Type Iii, Yeast Small Ubiquitin-Like Modifier, Smt3, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. N. Gilbreth, K. Truong, I. Madu, A. Koide, J. B. Wojcik, N. S. Li, J. A. Piccirilli, Y. Chen, S. Koide
Isoform-Specific Monobody Inhibitors Of Small Ubiquitin-Related Modifiers Engineered Using Structure-Guided Library Design.
Proc. Natl. Acad. Sci. Usa V. 108 7751 2011
PubMed-ID: 21518904 | Reference-DOI: 10.1073/PNAS.1102294108

Molecule 1 - UBIQUITIN-LIKE PROTEIN SMT3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SMT3, YDR510W, D9719.15
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	YEAST SMALL UBIQUITIN-LIKE MODIFIER (SUMO)

Molecule 2 - MONOBODY YSMB-1
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ARTIFICIAL GENE
	Organism Taxid	:	32630

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:21 , HIS A:23 , ASN A:25 , LYS A:38 , ASP A:85 , GLU C:47	BINDING SITE FOR RESIDUE GOL A 99
2	AC2	SOFTWARE	SER A:32 , SER A:33 , GLU A:34 , HOH A:107 , SER C:86	BINDING SITE FOR RESIDUE GOL A 100
3	AC3	SOFTWARE	TYR A:67 , ASP A:68 , ASP A:87 , ILE A:88 , SER C:25 , HOH C:118	BINDING SITE FOR RESIDUE GOL A 101
4	AC4	SOFTWARE	ASP A:68 , ILE A:70 , THR D:49	BINDING SITE FOR RESIDUE GOL A 102
5	AC5	SOFTWARE	ASP A:75 , HOH A:116 , HOH A:117 , TYR D:78 , TYR D:79	BINDING SITE FOR RESIDUE GOL A 103
6	AC6	SOFTWARE	ASP B:75 , GLY C:41 , TYR C:78 , TYR C:79 , HOH C:100	BINDING SITE FOR RESIDUE GOL C 95
7	AC7	SOFTWARE	HOH A:109 , PRO C:5 , THR C:6 , ASP C:23 , ALA C:24 , SER C:25 , SER C:26 , TYR C:32 , HOH C:116	BINDING SITE FOR RESIDUE GOL C 96
8	AC8	SOFTWARE	ASN C:91 , TYR C:92 , ARG C:93	BINDING SITE FOR RESIDUE GOL C 97

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

Asymmetric Unit

No.	Residues
1	Ile A:96	-	Gly A:97
2	Val C:4	-	Pro C:5
3	Ser D:3	-	Val D:4
4	Val D:4	-	Pro D:5
5	Ser D:27	-	Ser D:28

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	2	A:22-97 B:22-94

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	1	A:22-97 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	1	- B:22-94

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR510W	1	YDR510W.1	IV:1469393-1469698	306	SMT3_YEAST	1-101	101	2	A:19-97 B:22-94	79 73

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:79
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:79
                                    28        38        48        58        68        78        88         
            SMT3_YEAST   19 KPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG 97
               SCOP domains d3qhta_ A: automated matches                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeee....hhhhhhhhhhhh..hhh.eeeee..ee...............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBIQUITIN_2  PDB: A:22-97 UniProt: 22-98                                     PROSITE
               Transcript 1 Exon 1.1  PDB: A:19-97 UniProt: 1-101 [INCOMPLETE]                              Transcript 1
                  3qht A 19 KPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG 97
                                    28        38        48        58        68        78        88

Chain B from PDB  Type:PROTEIN  Length:73
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:73
                                    31        41        51        61        71        81        91   
            SMT3_YEAST   22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE 94
               SCOP domains d3qhtb_ B: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----ubiquitin-3qhtB01 B:27-94                                            Pfam domains (1)
           Pfam domains (2) -----ubiquitin-3qhtB02 B:27-94                                            Pfam domains (2)
         Sec.struct. author ..eeeeee....eeeeee.....hhhhhhhhhhh...hhhhheeee..ee...............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: B:22-94 UniProt: 22-98                                  PROSITE
               Transcript 1 Exon 1.1  PDB: B:22-94 UniProt: 1-101 [INCOMPLETE]                        Transcript 1
                  3qht B 22 THINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE 94
                                    31        41        51        61        71        81        91

Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains d3qhtc_ C: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeee.........eeeeeeee.......eeeeee....eeee.......eeeeeeeeeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3qht C  2 SSVPTKLEVVAATPTSLLISWDASSSSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYAYYSYYDLYYSYSPSSINYRT 94
                                    11        21        31        41        51        61        71        81        91

Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains d3qhtd_ D: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeee.........eeeeeeee.......eeeeee....eeee.......eeeeeeeeeeee..eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3qht D  2 SSVPTKLEVVAATPTSLLISWDASSSSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYAYYSYYDLYYSYSPSSINYRT 94
                                    11        21        31        41        51        61        71        81        91

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

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ubiquitin (279)

Family: ubiquitin (99)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (8)

1a	ubiquitin-3qhtB01	B:27-94
1b	ubiquitin-3qhtB02	B:27-94

Asymmetric Unit(hide GO term definitions)

Chain A,B (SMT3_YEAST | Q12306)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0000070	mitotic sister chromatid segregation	The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	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:0005940	septin ring	A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

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	Cis Peptide Bonds
		Ile A:96 - Gly A:97	[ RasMol ]
		Ser D:27 - Ser D:28	[ RasMol ]
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	3qht
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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