3HQM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURES OF SPOP-SUBSTRATE COMPLEXES: INSIGHTS INTO MOLECULAR ARCHITECTURES OF BTB-CUL3 UBIQUITIN LIGASES: SPOPMATHX-CISBC2

Authors :   M. Zhuang, B. A. Schulman

Date :   07 Jun 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

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

Keywords :   Ubiquitin, E3, Spop, Math, Ci, Nucleus, Ubl Conjugation Pathway, Developmental Protein, Dna-Binding, Metal-Binding, Segmentation Polarity Protein, Zinc-Finger, 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

Molecule 1 - SPECKLE-TYPE POZ PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 28-166
	Gene	:	SPOP
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HIB HOMOLOG 1, ROADKILL HOMOLOG 1

Molecule 2 - PROTEIN CUBITUS INTERRUPTUS
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 1356-1367
	Synthetic	:	YES

		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, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:13 , CYS A:44 , ARG A:45 , GLU A:46 , HOH A:334 , ARG B:138	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	ILE A:137 , ARG A:138 , HOH B:16 , CYS B:44 , ARG B:45 , GLU B:46 , HOH B:167	BINDING SITE FOR RESIDUE SO4 B 2
3	AC3	SOFTWARE	HOH A:208 , HOH A:215 , HOH A:273 , HOH A:322 , HOH B:5 , TYR B:34 , TRP B:36 , SER B:54 , SER B:55 , HOH B:247	BINDING SITE FOR RESIDUE SO4 B 3
4	AC4	SOFTWARE	HOH A:6 , TYR A:34 , TRP A:36 , SER A:54 , SER A:55 , HOH A:195 , HOH A:248 , HOH A:318	BINDING SITE FOR RESIDUE SO4 A 4

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

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

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

Asymmetric Unit (1, 2)

	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

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MATH	PS50144	MATH/TRAF domain profile.	SPOP_HUMAN	31-161	1	A:31-161 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MATH	PS50144	MATH/TRAF domain profile.	SPOP_HUMAN	31-161	1	- B:31-161

Asymmetric Unit (4, 8)

	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	0	-	-
1.10d	ENST00000393328	10d	ENSE00002189108	chr17:47699429-47699308	122	SPOP_HUMAN	27-67	41	2	A:28-67 (gaps) B:29-67 (gaps)	40 39
1.12c	ENST00000393328	12c	ENSE00002169279	chr17:47696747-47696596	152	SPOP_HUMAN	67-118	52	2	A:67-118 (gaps) B:67-118	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:161-165 B:161-164	5 4
1.17	ENST00000393328	17	ENSE00002159579	chr17:47685291-47685236	56	SPOP_HUMAN	220-238	19	0	-	-
1.18b	ENST00000393328	18b	ENSE00000819783	chr17:47684734-47684612	123	SPOP_HUMAN	239-279	41	0	-	-
1.19b	ENST00000393328	19b	ENSE00000736281	chr17:47679369-47679227	143	SPOP_HUMAN	280-327	48	0	-	-
1.20g	ENST00000393328	20g	ENSE00002070429	chr17:47677884-47676246	1639	SPOP_HUMAN	327-374	48	0	-	-

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:135
 aligned with SPOP_HUMAN | O43791 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:138
                                    37        47        57        67        77        87        97       107       117       127       137       147       157        
          SPOP_HUMAN     28 KVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ  165
               SCOP domains d3hqma_ A: Speckle-type poz prote  in SPOP                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhh.......ee.......--...eeeeeee....hhhhh.eeeeeeeeee..-..eeeeeeeeee.....eeeeee....eee....eeeeeeeeehhhhhhhhhh.hhhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---MATH  PDB: A:31-161 UniProt: 31-161                                                                                                ---- PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: A:28-67 (gaps)         --------------------------------------------------Exon 1.13b  PDB: A:118-160 UniProt: 118-1601.16c Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.12c  PDB: A:67-118 (gaps) UniProt: 67-118    ----------------------------------------------- Transcript 1 (2)
                3hqm A   28 KVVKFSYMWTINNFSFCREEMGEVIKSSTFSSG--DKLKWCLRVNPKGLDEESKDYLSLYLLLVSCP-SEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQ  165
                                    37        47        57  |  |  67        77        87      | 97       107       117       127       137       147       157        
                                                           60 63                             94 |                                                                     
                                                                                               96

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with SPOP_HUMAN | O43791 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:136
                                    38        48        58        68        78        88        98       108       118       128       138       148       158      
          SPOP_HUMAN     29 VVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVV  164
               SCOP domains d3hqmb_ B: Speckle-type poz pro    tein SPOP                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhh.......ee......----..eeeeeee....hhhhh.eeeeeeeeee.....eeeeeeeeee.....eeeeee....eee....eeeeeeeeehhhhhhhhhh.hhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --MATH  PDB: B:31-161 UniProt: 31-161                                                                                                --- PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: B:29-67 (gaps)        --------------------------------------------------Exon 1.13b  PDB: B:118-160 UniProt: 118-1601.16 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.12c  PDB: B:67-118 UniProt: 67-118           ---------------------------------------------- Transcript 1 (2)
                3hqm B   29 VVKFSYMWTINNFSFCREEMGEVIKSSTFSS----KLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVV  164
                                    38        48        58|    |  68        78        88        98       108       118       128       138       148       158      
                                                         59   64

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with CI_DROME | P19538 from UniProtKB/Swiss-Prot  Length:1397

    Alignment length:7
            CI_DROME   1360 PDVSSST 1366
               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
                3hqm C 1360 PDVSSST 1366

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with CI_DROME | P19538 from UniProtKB/Swiss-Prot  Length:1397

    Alignment length:7
            CI_DROME   1360 PDVSSST 1366
               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
                3hqm D 1360 PDVSSST 1366

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 beta proteins (24004)

Fold: TRAF domain-like (34)

Superfamily: TRAF domain-like (34)

Family: MATH domain (26)

Protein domain: Speckle-type poz protein SPOP (8)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d3hqma_	A:
1b	d3hqmb_	B:

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

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

Asymmetric 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.

Chain C,D (CI_DROME | P19538)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	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: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:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0001205	transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0007350	blastoderm segmentation	The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo.
	GO:0035017	cuticle pattern formation	The regionalization process that gives rise to the patterns of cell differentiation in the cuticle.
	GO:0048813	dendrite morphogenesis	The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
	GO:0008544	epidermis development	The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
	GO:0048592	eye morphogenesis	The process in which the anatomical structures of the eye are generated and organized.
	GO:0035224	genital disc anterior/posterior pattern formation	The establishment, maintenance and elaboration of the anterior/posterior axis of the genital disc. An anterior and posterior compartment form in each of the three genital disc primoridia (the female genital disc primordium, the male genital disc primordium and the anal primordium).
	GO:0060914	heart formation	The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.
	GO:0035217	labial disc development	Progression of the labial imaginal disc over time, from its initial formation through to its metamorphosis to form adult structures including parts of the proboscis.
	GO:0002385	mucosal immune response	An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0048666	neuron development	The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0030707	ovarian follicle cell development	The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster.
	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0030858	positive regulation of epithelial cell differentiation	Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0007346	regulation of mitotic cell cycle	Any process that modulates the rate or extent of progress through the mitotic cell cycle.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007367	segment polarity determination	Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products.
	GO:0007224	smoothened signaling pathway	A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
	GO:0035277	spiracle morphogenesis, open tracheal system	The process in which the anatomical structures of a spiracle are generated and organized. Spiracles are the openings in the insect open tracheal system; externally they connect to the epidermis and internally they connect to the tracheal trunk.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0048100	wing disc anterior/posterior pattern formation	The establishment, maintenance and elaboration of the anterior/posterior axis of the wing disc, a precursor to the wing.
cellular component
	GO:0035301	Hedgehog signaling complex	A multiprotein complex that binds microtubules in a Hedgehog-dependent manner, and is required for signal transduction by members of the Hedgehog family of proteins. The core components of the complex are the serine/threonine protein kinase Fused, the kinesin motor protein Costal2 (Cos2), and a zinc finger transcription factor (Gli family members in humans, and Cubitus interruptus (Ci) in Drosophila).
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

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

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Ligands, Modified Residues, Ions (1, 4)

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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