2V24 - JenaLib

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Title :   STRUCTURE OF THE HUMAN SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN SSB-4

Authors :   J. Uppenberg, A. Bullock, T. Keates, P. Savitsky, A. C. W. Pike, E. Ugoch G. Bunkoczi, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, S. Knapp

Date :   31 May 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Protein-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, A. Low, T. D. Sharpe, J. Uppenberg, S. Yao, Z. Kuang, P. Savitsky, R. S. Lewis, S. E. Nicholson, R. S. Norton, A. Bullock
Structural Basis For Par-4 Recognition By The Spry Domain- And Socs Box-Containing Proteins Spsb1, Spsb2, And Spsb4.
J. Mol. Biol. V. 401 389 2010
PubMed-ID: 20561531 | Reference-DOI: 10.1016/J.JMB.2010.06.017

Molecule 1 - SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28-233
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SSB-4

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:76 , ARG A:77 , HIS A:78 , HIS A:219 , GLU A:233	BINDING SITE FOR RESIDUE NI A1234

(no "SS Bond" information available for 2V24)

Asymmetric Unit

No.	Residues
1	Tyr A:161	-	Pro A:162

(no "SAP(SNP)/Variant" information available for 2V24)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B302_SPRY	PS50188	B30.2/SPRY domain profile.	SPSB4_HUMAN	34-233	1	A:34-233
2	SOCS	PS50225	SOCS box domain profile.	SPSB4_HUMAN	233-273	1	A:233-233

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B302_SPRY	PS50188	B30.2/SPRY domain profile.	SPSB4_HUMAN	34-233	2	A:34-233
2	SOCS	PS50225	SOCS box domain profile.	SPSB4_HUMAN	233-273	2	A:233-233

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000310546	1	ENSE00001205934	chr3:140770244-140770834	591	SPSB4_HUMAN	-	0	0	-	-
1.2a	ENST00000310546	2a	ENSE00001205942	chr3:140784794-140785640	847	SPSB4_HUMAN	1-232	232	1	A:33-232 (gaps)	200
1.7c	ENST00000310546	7c	ENSE00002063647	chr3:140865984-140867453	1470	SPSB4_HUMAN	232-273	42	1	A:232-233	2

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)
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Chain A from PDB  Type:PROTEIN  Length:197
 aligned with SPSB4_HUMAN | Q96A44 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:201
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
          SPSB4_HUMAN    33 RPARLDQLLDMPAAGLAVQLRHAWNPEDRSLNVFVKDDDRLTFHRHPVAQSTDGIRGKVGHARGLHAWQINWPARQRGTHAVVGVATARAPLHSVGYTALVGSDAESWGWDLGRSRLYHDGKNQPGVAYPAFLGPDEAFALPDSLLVVLDMDEGTLSFIVDGQYLGVAFRGLKGKKLYPVVSAVWGHCEVTMRYINGLDPE 233
               SCOP domains d2v24a_ A: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------SPRY-2v24A01 A:95-229                                                                                                                  ---- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhh.eeeeee...eeee..eeeeeee.....eeeeeee.......eeeeeee.hhhhh....eeeee......eee...........eeeee....eee..----..ee...............eeeeeee....eeeeee..eeeeeee........eeeeee.....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -B302_SPRY  PDB: A:34-233 UniProt: 34-233                                                                                                                                                                 PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:33-232 (gaps) UniProt: 1-232 [INCOMPLETE]                                                                                                                                             - Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 2v24 A  33 RPARLDQLLDMPAAGLAVQLRHAWNPEDRSLNVFVKDDDRLTFHRHPVAQSTDGIRGKVGHARGLHAWQINWPARQRGTHAVVGVATARAPLHSVGYTALVGSDAESWGWDLGRSRLYHD----PGVAYPAFLGPDEAFALPDSLLVVLDMDEGTLSFIVDGQYLGVAFRGLKGKKLYPVVSAVWGHCEVTMRYINGLDPE 233
                                    42        52        62        72        82        92       102       112       122       132       142       152    |  162       172       182       192       202       212       222       232 
                                                                                                                                                 152  157

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: SPRY domain (9)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (1)

d2v24a_

(no "CATH Domain" information available for 2V24)

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SPRY] (6)

Family: SPRY (6)

Homo sapiens (Human) (5)

SPRY-2v24A01

A:95-229

Asymmetric Unit(hide GO term definitions)

Chain A (SPSB4_HUMAN | Q96A44)

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: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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:161 - Pro A:162	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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