2FNJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A B30.2/SPRY DOMAIN-CONTAINING PROTEIN GUSTAVUS IN COMPLEX WITH ELONGIN B AND ELONGIN C

Authors :   J. S. Woo, B. H. Oh

Date :   11 Jan 06 (Deposition) - 21 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Beta-Sandwich, Lectin-Like, B30. 2, Spry, Protein Transport/Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Woo, J. H. Imm, C. K. Min, K. J. Kim, S. S. Cha, B. H. Oh
Structural And Functional Insights Into The B30. 2/Spry Domain
Embo J. V. 25 1353 2006
PubMed-ID: 16498413 | Reference-DOI: 10.1038/SJ.EMBOJ.7600994
(for further references see the PDB file header)

Molecule 1 - CG2944-PF, ISOFORM F
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 28-253
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	GUSTAVUS

Molecule 2 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B, SIII P18, ELONGIN B, ELOB, ELONGIN 18 KDA SUBUNIT

Molecule 3 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 17-112
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C, SIII P15, ELONGIN C, ELOC, ELONGIN 15 KDA SUBUNIT, STROMAL MEMBRANE-ASSOCIATED PROTEIN SMAP1B HOMOLOG

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2FNJ)

(no "Site" information available for 2FNJ)

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:165	-	Pro A:166

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	ELOB_MOUSE	1-66	1	B:1-66
2	B302_SPRY	PS50188	B30.2/SPRY domain profile.	GUS_DROME	36-233	1	A:38-235
3	SOCS	PS50225	SOCS box domain profile.	GUS_DROME	223-279	1	A:225-251

(no "Exon" information available for 2FNJ)

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:217
 aligned with GUS_DROME | A1Z6E0 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:217
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
            GUS_DROME    33 FVKPARIDILLDMPPASRDLQLKHSWNSEDRSLNIFVKEDDKLTFHRHPVAQSTDCIRGKVGLTKGLHIWEIYWPTRQRGTHAVVGVCTADAPLHSVGYQSLVGSTEQSWGWDLGRNKLYHDSKNCAGVTYPAILKNDEAFLVPDKFLVALDMDEGTLSFIVDQQYLGIAFRGLRGKKLYPIVSAVWGHCEITMRYIGGLDPEPLPLMDLCRRTIRQ 249
               SCOP domains d2fnja1 A:35-251 LD34464p                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...hhhhhhhh.eeeeee...eeee..eeeeeee.....eeeeeee.......eeeeeee.hhhhh....eeeee......eee...........eeeee....eeee.......ee...............eeeeeee....eeeeee..eeeeeee........eeeeee.....eeeeeeeeee.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---B302_SPRY  PDB: A:38-235 UniProt: 36-233                                                                                                                                                              ---------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOCS  PDB: A:225-251        PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fnj A  35 FVKPARIDILLDMPPASRDLQLKHSWNSEDRSLNIFVKEDDKLTFHRHPVAQSTDCIRGKVGLTKGLHIWEIYWPTRQRGTHAVVGVCTADAPLHSVGYQSLVGSTEQSWGWDLGRNKLYHDSKNCAGVTYPAILKNDEAFLVPDKFLVALDMDEGTLSFIVDQQYLGIAFRGLRGKKLYPIVSAVWGHCEITMRYIGGLDPEPLPLMDLCRRTIRQ 251
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ELOB_MOUSE | P62869 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
           ELOB_MOUSE     1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALRIEPFSSPPE  98
               SCOP domains d2fnjb1 B:1-98 Elongin B                                                                           SCOP domains
               CATH domains 2fnjB00 B:1-98 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh...........eeeeeee................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: B:1-66 UniProt: 1-66                            -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2fnj B   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALRIEPFSSPPE  98
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with ELOC_MOUSE | P83940 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:96
                                    26        36        46        56        66        76        86        96       106      
           ELOC_MOUSE    17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
               SCOP domains d2fnjc_ C: Elongin C                                                                             SCOP domains
               CATH domains 2fnjC00 C:17-112 Potassium Channe        l Kv1.1; Chain A                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhhhhh.--------.eee....hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2fnj C  17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGP--------NEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46  |      - |      66        76        86        96       106      
                                                           49       58

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 "Pfam Domain" information available for 2FNJ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GUS_DROME | A1Z6E0)

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).
biological process
	GO:0035017	cuticle pattern formation	The regionalization process that gives rise to the patterns of cell differentiation in the cuticle.
	GO:0046843	dorsal appendage formation	Establishment of the dorsal filaments, elaborate specializations of the chorion that protrude from the anterior end of the egg and facilitate embryonic respiration.
	GO:0007281	germ cell development	The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	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:0007314	oocyte anterior/posterior axis specification	Polarization of the oocyte along its anterior-posterior axis. An example of this is found in Drosophila melanogaster.
	GO:0007280	pole cell migration	The directed movement of a pole cell (germline progenitors in insects) from its site of production at the posterior pole of the embryo through to the site where the gonads will form.
	GO:0007315	pole plasm assembly	Establishment of the specialized cytoplasm found at the poles of the egg. An example of this is found in Drosophila melanogaster.
	GO:0045732	positive regulation of protein catabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
	GO:0007472	wing disc morphogenesis	The process in which the anatomical structures derived from the wing disc are generated and organized. This includes the transformation of a wing imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the wing hinge, wing blade and pleura.
cellular component
	GO:0031466	Cul5-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul5 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070449	elongin complex	A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3'-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0045495	pole plasm	Differentiated cytoplasm associated with a pole (animal, vegetal, anterior, or posterior) of an oocyte, egg or early embryo.

Chain B (ELOB_MOUSE | P62869)

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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0031462	Cul2-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul2 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
	GO:0031466	Cul5-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul5 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by an elongin-BC adaptor and a SOCS/BC box protein.
	GO:0030891	VCB complex	A protein complex that possesses ubiquitin ligase activity; the complex is usually pentameric; for example, in mammals the subunits are pVHL, elongin B, elongin C, cullin-2 (Cul2), and Rbx1.
	GO:0070449	elongin complex	A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3'-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits.
	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: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 (ELOC_MOUSE | P83940)

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:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0006511	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 a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:0070449	elongin complex	A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3'-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits.
	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
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 2fnj)

	Cis Peptide Bonds
		Tyr A:165 - Pro A:166	[ RasMol ]

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	2fnj
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	ELOB_MOUSE \| P62869	:	4jgh
	ELOC_MOUSE \| P83940	:	2jz3 4jgh
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1vcb	STRUCTRE OF A PROTEIN IN COMPLEX WITH ELONGIN B AND ELONGIN C

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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SCOP Domains (3, 3)

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Gene Ontology (31, 40)

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