3HQI - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURES OF SPOP-SUBSTRATE COMPLEXES: INSIGHTS INTO MOLECULAR ARCHITECTURES OF BTB-CUL3 UBIQUITIN LIGASES: SPOPMATHX/BTB/3-BOX-PUCSBC1

Authors :   M. Zhuang, B. A. Schulman

Date :   07 Jun 09 (Deposition) - 20 Oct 09 (Release) - 27 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Spop, E3, Ubiquitin, Puckered, Nucleus, Ubl Conjugation Pathway, Protein Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zhuang, M. F. Calabrese, J. Liu, M. B. Waddell, A. Nourse, M. Hammel, D. J. Miller, H. Walden, D. M. Duda, S. N. Seyedin, T. Hoggard, J. W. Harper, K. P. White, B. A. Schulman
Structures Of Spop-Substrate Complexes: Insights Into Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases.
Mol. Cell V. 36 39 2009
PubMed-ID: 19818708 | Reference-DOI: 10.1016/J.MOLCEL.2009.09.022
(for further references see the PDB file header)

Molecule 1 - SPECKLE-TYPE POZ PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 28-329
	Gene	:	SPOP
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HIB HOMOLOG 1, ROADKILL HOMOLOG 1

Molecule 2 - PUCSBC1
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3HQI)

(no "Site" information available for 3HQI)

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

(no "Cis Peptide Bond" information available for 3HQI)

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MATH	PS50144	MATH/TRAF domain profile.	SPOP_HUMAN	31-161	2	A:31-161 B:31-161
2	BTB	PS50097	BTB domain profile.	SPOP_HUMAN	200-262	2	A:200-262 B:200-262

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000393328	1d	ENSE00002053260	chr17:47755472-47755295	178	SPOP_HUMAN	-	0	0	-	-
1.2	ENST00000393328	2	ENSE00002056951	chr17:47753378-47753257	122	SPOP_HUMAN	-	0	0	-	-
1.8d	ENST00000393328	8d	ENSE00002153086	chr17:47700238-47700095	144	SPOP_HUMAN	1-26	26	2	A:26-27 B:26-27	2 2
1.10d	ENST00000393328	10d	ENSE00002189108	chr17:47699429-47699308	122	SPOP_HUMAN	27-67	41	2	A:28-67 (gaps) B:28-67 (gaps)	40 40
1.12c	ENST00000393328	12c	ENSE00002169279	chr17:47696747-47696596	152	SPOP_HUMAN	67-118	52	2	A:67-118 (gaps) B:67-118 (gaps)	52 52
1.13b	ENST00000393328	13b	ENSE00001746781	chr17:47696470-47696343	128	SPOP_HUMAN	118-160	43	2	A:118-160 B:118-160	43 43
1.16c	ENST00000393328	16c	ENSE00000819785	chr17:47688819-47688642	178	SPOP_HUMAN	161-220	60	2	A:161-220 B:161-220 (gaps)	60 60
1.17	ENST00000393328	17	ENSE00002159579	chr17:47685291-47685236	56	SPOP_HUMAN	220-238	19	2	A:220-238 (gaps) B:220-238 (gaps)	19 19
1.18b	ENST00000393328	18b	ENSE00000819783	chr17:47684734-47684612	123	SPOP_HUMAN	239-279	41	2	A:239-279 B:239-279	41 41
1.19b	ENST00000393328	19b	ENSE00000736281	chr17:47679369-47679227	143	SPOP_HUMAN	280-327	48	2	A:280-327 B:280-327	48 48
1.20g	ENST00000393328	20g	ENSE00002070429	chr17:47677884-47676246	1639	SPOP_HUMAN	327-374	48	2	A:327-329 B:327-329	3 3

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:294
 aligned with SPOP_HUMAN | O43791 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:314
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
           SPOP_HUMAN    16 GPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQAHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYALERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHA 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .e----------eeeeeeeeeee.hhhhh.......ee......--....eeeeeee.....--...eeeeeeeeee...-.eeeeeeeeee.....eeeeee....eee....eeeeeeeeehhhhhhhhhh.hhhhheeeeeeeeeeee...ee.............hhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhh..-----...eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------MATH  PDB: A:31-161 UniProt: 31-161                                                                                                --------------------------------------BTB  PDB: A:200-262 UniProt: 200-262                           ------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8d  Exon 1.10d  PDB: A:28-67 (gaps)          --------------------------------------------------Exon 1.13b  PDB: A:118-160 UniProt: 118-160Exon 1.16c  PDB: A:161-220 UniProt: 161-220                 ------------------Exon 1.18b  PDB: A:239-279               Exon 1.19b  PDB: A:280-327 UniProt: 280-327     -- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.12c  PDB: A:67-118 (gaps) UniProt: 67-118    -----------------------------------------------------------------------------------------------------Exon 1.17          ----------------------------------------------------------------------------------------1.2 Transcript 1 (2)
                 3hqi A  26 GS----------KVVKFSYMWTINNFSFCREEMGEVIKSSTFSS--NDKLKWCLRVNPKGLD--SKDYLSLYLLLVSCPK-EVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQAHKAILAARSPVFSAMFEH-----KKNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYALERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHA 329
                             |       -  |     35        45        55   |  | 65        75 |  |   85        95 |     105       115       125       135       145       155       165       175       185       195       205       215       225     |   - |     245       255       265       275       285       295       305       315       325    
                             |         28                             59 62             77 80             95 |                                                                                                                                   231   237                                                                                            
                            27                                                                              97

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with SPOP_HUMAN | O43791 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:314
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
           SPOP_HUMAN    16 GPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQAHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYALERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHA 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .e----------eeeeeeeeeee.hhhhh.......ee...ee..---..eeeeeee.....--...eeeeeeeeee...-.eeeeeeeeee.....eeeeee....eee....eeeeeeeeehhhhhhhhhh.hhhhheeeeeeeeeeee..--------........hhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhh..------..eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------MATH  PDB: B:31-161 UniProt: 31-161                                                                                                --------------------------------------BTB  PDB: B:200-262 UniProt: 200-262                           ------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8d  Exon 1.10d  PDB: B:28-67 (gaps)          --------------------------------------------------Exon 1.13b  PDB: B:118-160 UniProt: 118-160Exon 1.16c  PDB: B:161-220 (gaps) UniProt: 161-220          ------------------Exon 1.18b  PDB: B:239-279               Exon 1.19b  PDB: B:280-327 UniProt: 280-327     -- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.12c  PDB: B:67-118 (gaps) UniProt: 67-118    -----------------------------------------------------------------------------------------------------Exon 1.17          ----------------------------------------------------------------------------------------1.2 Transcript 1 (2)
                 3hqi B  26 GS----------KVVKFSYMWTINNFSFCREEMGEVIKSSTFSSG---KLKWCLRVNPKGLD--SKDYLSLYLLLVSCPK-EVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQDSV--------NMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQAHKAILAARSPVFSAMFEH------KNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYALERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHA 329
                             |       -  |     35        45        55    |   65        75 |  |   85        95 |     105       115       125       135       145       155       165  |      - |     185       195       205       215       225     |   -  |    245       255       265       275       285       295       305       315       325    
                            27         28                              60  64           77 80             95 |                                                                    168      177                                                   231    238                                                                                           
                                                                                                            97

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3hqi C  97 EVTSTT 102

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3hqi D  97 EVTSTT 102

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 '\|'

(no "SCOP Domain" information available for 3HQI)

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

(no "Pfam Domain" information available for 3HQI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SPOP_HUMAN | O43791)

molecular function
	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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0031463	Cul3-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3hqi)

	Sites
(no "Sites" information available for 3hqi)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hqi)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3hqi
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SPOP_HUMAN \| O43791
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SPOP_HUMAN \| O43791
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SPOP_HUMAN \| O43791	:	2cr2 3hqh 3hql 3hqm 3hsv 3htm 3hu6 3ivb 3ivq 3ivv 4eoz 4hs2 4j8z 4o1v

(no "Related Entries Specified in the PDB File" available for 3HQI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (9, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File