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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SOCS-4 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 2.55A RESOLUTION

Authors :   J. E. Debreczeni, A. Bullock, E. Papagrigoriou, A. Turnbull, A. C. W. Pi F. Gorrec, F. Von Delft, M. Sundstrom, C. Arrowsmith, J. Weigelt, A. E S. Knapp

Date :   26 Jul 06 (Deposition) - 02 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Signal Transduction Inhibitor, Growth Regulation, Signal Transduction, Sh2 Domain, Transcription, Nuclear Protein, Ubl Conjugation Pathway, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. N. Bullock, M. C. Rodriguez, J. E. Debreczeni, Z. Songyang, S. Knapp
Structure Of The Socs4-Elonginb/C Complex Reveals A Distinct Socs Box Interface And The Molecular Basis For Socs-Dependent Egfr Degradation.
Structure V. 15 1493 2007
PubMed-ID: 17997974 | Reference-DOI: 10.1016/J.STR.2007.09.016

Molecule 1 - SUPPRESSOR OF CYTOKINE SIGNALING 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector	:	P11
	Fragment	:	RESIDUES 274-437
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SOCS-4 ELONGIN B, C COMPLEX, SOCS-4, SOCS-7, SUPPRESSOR OF CYTOKINE SIGNALING 7

Molecule 2 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector	:	P11
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	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 Cell Line	:	BL21(DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector	:	P11
	Fragment	:	RESIDUES 17-112
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C, SIII P15, ELONGIN-C, ELOC, ELONGIN 15 KDA SUBUNIT

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:313 , GLN A:315 , TYR A:318 , EDO A:1431 , HOH A:2022 , HOH A:2023	BINDING SITE FOR RESIDUE NA A1430
2	AC2	SOFTWARE	ASP A:312 , SER A:313 , TYR A:318 , LEU A:319 , GLU A:421 , NA A:1430 , HOH A:2020	BINDING SITE FOR RESIDUE EDO A1431

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

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

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	ELOB_HUMAN	1-66	1	B:1-66
2	SH2	PS50001	Src homology 2 (SH2) domain profile.	SOCS4_HUMAN	286-381	1	A:286-381
3	SOCS	PS50225	SOCS box domain profile.	SOCS4_HUMAN	376-425	1	A:376-425

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1g	ENST00000284811	1g	ENSE00002103151	chr8:74884341-74884277	65	ELOC_HUMAN	-	0	0	-	-
1.6	ENST00000284811	6	ENSE00001087342	chr8:74872053-74872000	54	ELOC_HUMAN	1-2	2	0	-	-
1.7	ENST00000284811	7	ENSE00001016720	chr8:74868289-74868146	144	ELOC_HUMAN	2-50	49	1	C:17-46	30
1.10d	ENST00000284811	10d	ENSE00001424822	chr8:74859055-74858636	420	ELOC_HUMAN	50-112	63	1	C:58-112	55

2.1b	ENST00000395472	1b	ENSE00001814919	chr14:55493948-55494189	242	SOCS4_HUMAN	-	0	0	-	-
2.3b	ENST00000395472	3b	ENSE00001933327	chr14:55509670-55516206	6537	SOCS4_HUMAN	1-470	470	1	A:267-429	163

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:163
 aligned with SOCS4_HUMAN | Q8WXH5 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:163
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426   
          SOCS4_HUMAN   267 QIDYVHCLVPDLLQINNNPCYWGVMDKYAAEALLEGKPEGTFLLRDSAQEDYLFSVSFRRYSRSLHARIEQWNHNFSFDAHDPCVFHSPDITGLLEHYKDPSACMFFEPLLSTPLIRTFPFSLQHICRTVICNCTTYDGIDALPIPSSMKLYLKEYHYKSKVR 429
               SCOP domains -------d2izva2 A:274-385 Suppressor of cytokine signaling 4, SOCS-4                                                    d2izva1 A:386-429                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhh..eeee.hhhhhhhhhh.....eeeeee.......eeeeeee..eeeeee.eee..eee............hhhhhhhhh.hhhhh........ee.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------SH2  PDB: A:286-381 UniProt: 286-381                                                            ------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------SOCS  PDB: A:376-425 UniProt: 376-425             ---- PROSITE (2)
               Transcript 2 Exon 2.3b  PDB: A:267-429 UniProt: 1-470 [INCOMPLETE]                                                                                                               Transcript 2
                 2izv A 267 NLYFQSMLVPDLLQINNNPCYWGVMDKYAAEALLEGKPEGTFLLRDSAQEDYLFSVSFRRYSRSLHARIEQWNHNFSFDAHDPCVFHSPDITGLLEHYKDPSACMFFEPLLSTPLIRTFPFSLQHICRTVICNCTTYDGIDALPIPSSMKLYLKEYHYKSKVR 429
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with ELOB_HUMAN | Q15370 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           ELOB_HUMAN     1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKP 105
               SCOP domains d2izvb_ B: automated matches                                                                              SCOP domains
               CATH domains 2izvB00 B:1-105 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee......................eeeeeeeee..ee..............hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: B:1-66 UniProt: 1-66                            --------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2izv B   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKP 105
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with ELOC_HUMAN | Q15369 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:96
                                    26        36        46        56        66        76        86        96       106      
           ELOC_HUMAN    17 MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
               SCOP domains d2izvc_ C: Elongin C                                                                             SCOP domains
               CATH domains 2izvC00 C:17-112 Potassium Cha           nnel Kv1.1; Chain A                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhh.-----------.eee....hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) ---------------------------------Exon 1.10d  PDB: C:58-112 UniProt: 50-112 [INCOMPLETE]          Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: C:17-46            -------------------------------------------------------------- Transcript 1 (2)
                 2izv C  17 MYVKLISSDGHEFIVKREHALTSGTIKAML-----------NEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    26        36        46         - |      66        76        86        96       106      
                                                        46          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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Potassium Channel Kv1.1; Chain A (53)

Homologous Superfamily: Potassium Channel Kv1.1; Chain A (53)

Human (Homo sapiens) (30)

2izvC00

C:17-112

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Human (Homo sapiens) (177)

2izvB00

B:1-105

(no "Pfam Domain" information available for 2IZV)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SOCS4_HUMAN | Q8WXH5)

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:0004860	protein kinase inhibitor activity	Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0046426	negative regulation of JAK-STAT cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
	GO:0007175	negative regulation of epidermal growth factor-activated receptor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.
	GO:0009968	negative regulation of signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of 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.
	GO:0040008	regulation of growth	Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (ELOB_HUMAN | Q15370)

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:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	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: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.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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 (ELOC_HUMAN | Q15369)

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:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	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: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: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.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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
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1lm8	STRUCTURE OF A HIF-1A-PVHL-ELONGINB- ELONGINC COMPLEX
1lqb	CRYSTAL STRUCTURE OF A HYDROXYLATED HIF-1 ALPHA PEPTIDEBOUND TO THE PVHL/ELONGIN-C/ ELONGIN-B COMPLEX
1vcb	THE VHL-ELONGINC-ELONGINB STRUCTURE
2c9w	CRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 1.9A RESOLUTION

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

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Exons (3, 3)

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SCOP Domains (4, 4)

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Gene Ontology (32, 44)

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